Lipid Formulated Compositions and Methods for Inhibiting Expression of a Gene from the Ebola Virus

ABSTRACT

The invention relates to lipid formulated double-stranded ribonucleic acid (dsRNA) for inhibiting the expression of a gene from the Ebola virus.

RELATED APPLICATIONS

This application claims the benefit of U.S. provisional application 61/234,236, filed Aug. 14, 2009, U.S. provisional application 61/242,732, filed Sep. 15, 2009, and U.S. provisional application 61/259,106, filed Nov. 6, 2009, each of which is hereby incorporated by reference for all purposes.

GOVERNMENT SUPPORT

This invention was made with government support under contract number HHSN266200600012C, ADB N01-AI-60012, awarded by the National Institute of Allergy and Infectious Diseases/National Institutes of Health/Department of Health and Human Services (NIAID/NIH/DHHS). The government has certain rights in the invention.

REFERENCE TO A SEQUENCE LISTING

This application includes a Sequence Listing submitted electronically as a text file named 17150PCT_sequencelisting.txt, created on Month, ______, 2010, with a size of ______ bytes. The sequence listing is incorporated by reference.

FIELD OF THE INVENTION

This invention relates to lipid formulated double-stranded ribonucleic acid (dsRNA), and its use in mediating RNA interference to inhibit the expression of one of the genes of the Ebola virus and the use of the dsRNA to treat pathological processes mediated by Ebola infection, such as systemic hemorrhage and multi-organ failure.

BACKGROUND OF THE INVENTION

Ebola Virus

Minus-strand (−) RNA viruses are major causes of human suffering that cause epidemics of serious human illness. In humans the diseases caused by these viruses include influenza (Orthomyxoviridae), mumps, measles, upper and lower respiratory tract disease (Paramyxoviridae), rabies (Rhabdoviridae), hemorrhagic fever (Filoviridae, Bunyaviridae and Arenaviridae), encephalitis (Bunyaviridae) and neurological illness (Bomaviridae). Virtually the entire human population is thought to be infected by many of these viruses.

The Ebola virus comes from the Filoviridae family, similar to the Marburg virus. It is named after the Ebola River in Zaire, Africa, near where the first outbreak was noted by Dr. Ngoy Mushola in 1976 after a significant outbreaks in both Yambuku, Zaire (now the Democratic Republic of the Congo), and Nzara, in western Sudan. Of 602 identified cases, there were 397 deaths.

The two strains identified in 1976 were named Ebola-Zaire (EBO-Z) and Ebola-Sudan (EBO-S). The outbreak in Sudan showed a lower fatality rate—50%—compared to the 90% mortality rate of the Zaire strain. In 1990, a second, similar virus was identified in Reston, Va. amongst monkeys imported from the Philippines, and was named Ebola-Reston.

Further outbreaks have occurred in Zaire/Congo (1995 and 2003), Gabon (1994, 1995 and 1996), and in Uganda (2000). A new subtype was identified from a single human case in the Côte d'Ivoire in 1994, EBO-CI.

Of around 1500 identified human Ebola infections, two-thirds of the patients have died. The animal (or other) reservoir which sustains the virus between outbreaks has not been identified.

Among humans, the Ebola virus is transmitted by direct contact with infected body fluids such as blood.

The incubation period of Ebola hemorrhagic fever varies from two days to four weeks. Symptoms are variable too, but the onset is usually sudden and characterised by high fever, prostration, myalgia, arthralgia, abdominal pains and headache. These symptoms progress to vomiting, diarrhea, oropharyngeal lesions, conjunctivitis, organ damage (notably the kidney and liver) by co-localized necrosis, proteinuria, and bleeding both internal and external, commonly through the gastrointestinal tract. Death or recovery to convalescence occurs within six to ten days of onset of symptomology.

The development of a successful therapeutic for Ebola virus is a long-sought and seemingly difficult endeavor. Although they cause only a few hundred deaths worldwide each year, filoviruses are considered a significant world health threat and have many of the characteristics commonly associated with biological weapons since they can be grown in large quantities, can be fairly stable, are highly infectious as an aerosol, and are exceptionally deadly. Filoviruses are relatively simple viruses of 19 Kb genomes and consist of seven genes which encode nucleoprotein (NP), glycoprotein (GP), four smaller viral proteins (VP24, VP30, VP35 and VP40), and the RNA-dependent RNA polymerase (L protein) all in a single strand of negative-sensed RNA. Administration of type I interferons, therapeutic vaccines, immune globulins, ribavirin, and other nucleoside analogues have been somewhat successful in rodent Ebola virus models, but not in nonhuman primate infection models.

In view of the severity of the diseases caused by (−) RNA viruses, in particular members of the Filoviridae family of viruses, and the lack of effective prevention or therapies, it is therefore an object of the present invention to provide therapeutic compounds and methods for treating a host infected with a (−) RNA virus.

siRNA

Double-stranded RNA molecules (dsRNA) have been shown to block gene expression in a highly conserved regulatory mechanism known as RNA interference (RNAi). WO 99/32619 (Fire et al.) discloses the use of a dsRNA of at least 25 nucleotides in length to inhibit the expression of genes in C. elegans. dsRNA has also been shown to degrade target RNA in other organisms, including plants (see, e.g., WO 99/53050, Waterhouse et al.; and WO 99/61631, Heifetz et al.), Drosophila (see, e.g., Yang, D., et al., Curr. Biol. (2000) 10:1191-1200), and mammals (see WO 00/44895, Limmer; and DE 101 00 586.5, Kreutzer et al.). This natural mechanism has now become the focus for the development of a new class of pharmaceutical agents for treating disorders that are caused by the aberrant or unwanted regulation of a gene.

Recent reports have indicated that in vitro, RNAi may show some promising in reducing Ebola replication and providing protection in guinea pigs (Geisbert, et al., The Journal of Infectious Diseases, 193 (2006), 1650-1657). However, the RNAi agents examined were not designed against all known Ebola strains and were not selected for stability and other properties needed for in vivo therapeutic RNAi agents. Accordingly, despite significant advances in the field of RNAi, there remains a need for an agent that can selectively and efficiently silence a gene in the Ebola virus using the cell's own RNAi machinery that has both high biological activity and in vivo stability, and that can effectively inhibit replication of the Ebola virus for use in treating pathological processes mediated by Ebola infection.

SUMMARY OF THE INVENTION

The invention provides a pharmaceutical composition including a double-stranded ribonucleic acid (dsRNA) and a lipid formulation, as well as methods for inhibiting the expression of the Ebola virus in a cell, mammal, or organism using such pharmaceutical composition. The invention also provides compositions and methods for treating pathological conditions and diseases caused by Ebola viral infection, such as systemic hemorrhage and multi-organ failure. The pharmaceutical composition featured in the invention includes an RNA strand (the antisense strand) having a region which is less than 30 nucleotides in length, generally 15-30 or 19-24 nucleotides in length, and is substantially complementary to at least part of an mRNA transcript of a gene from the Ebola virus.

In one embodiment, the invention provides a pharmaceutical composition including dsRNA molecules for inhibiting the expression of a gene of the Ebola virus and viral replication. The dsRNA comprises at least two sequences that are complementary to each other. The dsRNA comprises a sense strand comprising a first sequence and an antisense strand comprising a second sequence. The antisense strand comprises a nucleotide sequence which is substantially complementary to at least part of an mRNA encoded by a gene from the Ebola virus, and the region of complementarity is less than 30 nucleotides in length, generally 15-30 or 19-24 nucleotides in length. The pharmaceutical composition, upon contact with a cell infected with the Ebola virus, inhibits the expression of a gene from the Ebola virus by at least 40% compared to a control.

For example, the pharmaceutical compositions of the invention can include a first sequence of the dsRNA that is selected from the group consisting of the sense sequences of Table 2 and the second sequence selected from the group consisting of the antisense sequences of Table 2. The dsRNA molecules featured in the invention can include naturally occurring nucleotides or can include at least one modified nucleotide, such as a 2′-O-methyl modified nucleotide, a nucleotide comprising a 5′-phosphorothioate group, and a terminal nucleotide linked to a cholesteryl derivative. Alternatively, the modified nucleotide may be chosen from the group of: a 2′-deoxy-2′-fluoro modified nucleotide, a 2′-deoxy-modified nucleotide, a locked nucleotide, an abasic nucleotide, 2′-amino-modified nucleotide, 2′-alkyl-modified nucleotide, morpholino nucleotide, a phosphoramidate, and a non-natural base comprising nucleotide. Generally, such modified sequence will be based on a first sequence of said dsRNA selected from the group consisting of the sense sequences of Table 2 and a second sequence selected from the group consisting of the antisense sequences of Table 2. In other embodiments, the first sequence of the dsRNA consists of the sequence of SEQ ID NO:1027, and the second sequence consists of the sequence of SEQ ID NO:1028.

In another embodiment, the invention provides a pharmaceutical composition for inhibiting the replication of the Ebola virus in an organism, generally a human subject. The composition includes one or more of the dsRNA of the invention and a lipid formulation. In a related embodiment, the lipid formulation includes a cationic lipid of formula A:

where R₁ and R₂ are independently alkyl, alkenyl or alkynyl, each can be optionally substituted, and R₃ and R₄ are independently lower alkyl or R₃ and R₄ can be taken together to form an optionally substituted heterocyclic ring. In an embodiment, R₁ and R₂ of formula A are independently selected from olcoyl, pamitoyl, steroyl, or linolcyl. In another embodiment, R₁ and R₂ of formula A are both linolcyl. In another embodiment, R₃ and R₄ of formula A are methyl. In an embodiment, the cationic lipid of formula A is 2,2-Dilinolcyl-4-dimethylaminoethyl-[1,3]-dioxolane In an embodiment, the pharmaceutical composition can include a neutral lipid, a sterol, a PEG, or a PEG-modified lipid.

In another embodiment, the invention provides a method for inhibiting the expression of a gene in the Ebola virus in a cell, including the following steps:

-   -   (a) introducing into the cell a pharmaceutical composition         including a double-stranded ribonucleic acid (dsRNA) and a lipid         formulation, wherein the dsRNA includes at least two sequences         that are complementary to each other. The dsRNA includes a sense         strand having a first sequence and an antisense strand having a         second sequence. The antisense strand includes a region of         complementarity which is substantially complementary to at least         a part of an mRNA encoded by the Ebola virus, and wherein the         region of complementarity is less than 30 nucleotides in length,         generally 15-30 or 19-24 nucleotides in length, and optionally,         wherein the dsRNA, upon contact with a cell infected with the         Ebola virus, inhibits expression of a gene from the Ebola virus         by at least 40% compared to a control, such as in an assay         described herein (e.g., a fluorescence-based assay); and     -   (b) maintaining the cell produced in step (a) for a time         sufficient to obtain degradation of the mRNA transcript of a         Ebola gene, thereby inhibiting expression of a gene from the         Ebola virus in the cell.

In another embodiment, the invention provides methods for treating, preventing or managing pathological processes mediated by Ebola infection, such as systemic hemorrhage and multi-organ failure, comprising administering to a patient in need of such treatment, prevention or management a therapeutically or prophylactically effective amount of one or more of the pharmaceutical compositions of the invention. In certain related embodiments, the pharmaceutical composition is administered to said subject prior to infection with Ebola virus. In other embodiments, the pharmaceutical composition is administered to said subject after infection with Ebola virus. In yet other embodiments, the pharmaceutical composition is administered in a dose of about 1 to 5 mgs/kg, or about 2 to 3 mgs/kg (mgs/kg refers to mgs of siRNA per kg of subject weight). In still other embodiments, the pharmaceutical composition is administered to said subject by parenteral administration, e.g., intraperitoneally. In still other embodiments, the pharmaceutical composition is administered on a daily or semi-daily (e.g., bi-daily) basis for 7 to 10 days. In still other embodiments, the administration of said pharmaceutical composition reduces weight loss in said subject relative to the weight loss that would be observed after administration of a control composition or another treatment that did not include said pharmaceutical composition.

In one aspect, the invention provides for a method of increasing the life-span of a subject (e.g., a mammal, such as a human or nonhuman primate) infected with an Ebola virus. The method includes administering a pharmaceutical composition including a dsRNA and a lipid formulation to the subject, where the dsRNA includes an antisense RNA strand having a region which is less than 30 nucleotides in length, generally 15-30 or 19-24 nucleotides in length, and is substantially complementary to at least part of an mRNA transcript of a gene from the Ebola virus. The pharmaceutical composition is administered in an amount sufficient to increase the lifespan of the subject. In one embodiment, the pharmaceutical composition includes an antisense RNA strand having a region that is substantially complementary to at least part of an mRNA transcript of a gene selected from the VP30, VP35, NP, L, VP24, VP40 and GP genes. In one embodiment, the pharmaceutical composition includes an antisense RNA strand having a region that is substantially complementary to at least part of an mRNA transcript of the VP35 gene. In some embodiments, the subject does not experience a decrease in one or both of lymphocyte or platelet count after administration of the dsRNA. In other embodiments, the lymphocyte count of the subject is sustained. In other embodiments, the subject does not experience an increase in cytokine levels (e.g., IFN-alpha or TNF-alpha levels).

In another aspect, the invention features a method of decreasing viral titre in a subject (e.g., a mammal, such as a human or nonhuman primate) infected with an Ebola virus. The method includes administering a pharmaceutical composition including a dsRNA and a lipid formulation to the subject, where the dsRNA includes an antisense RNA strand having a region which is less than 30 nucleotides in length, generally 15-30 or 19-24 nucleotides in length, and is substantially complementary to at least part of an mRNA transcript of a gene from the Ebola virus. In one embodiment, the dsRNA includes an antisense RNA strand having a region that is substantially complementary to at least part of an mRNA transcript of the VP35 gene. In another embodiment, the subject does not experience a decrease in one or both of lymphocyte or platelet count after administration of the dsRNA. In other embodiments, the lymphocyte count of the subject is sustained. In other embodiments, the subject does not experience an increase in cytokine levels (e.g., IFN-alpha or TNF-alpha levels).

In another aspect, the invention features a method of sustaining lymphocyte or platelet count in a mammal (e.g., a human or nonhuman primate) infected with an Ebola virus. The method includes administering a pharmaceutical composition including a dsRNA and a lipid formulation to the subject, where the dsRNA includes an antisense RNA strand having a region which is less than 30 nucleotides in length, generally 15-30 or 19-24 nucleotides in length, and is substantially complementary to at least part of an mRNA transcript of a gene from the Ebola virus. In one embodiment, the dsRNA includes an antisense RNA strand having a region that is substantially complementary to at least part of an mRNA transcript of the VP35 gene. In other embodiments, the subject does not experience an increase in cytokine levels (e.g., IFN-alpha or TNF-alpha levels).

BRIEF DESCRIPTION OF THE FIGURES

FIG. 1 is a graph showing that siRNAs formulated with lipidoid LNP01 protected mice from a lethal Ebola virus challenge.

FIG. 2 is a graph showing that a single injection of a liposomally formulated siRNA delivered by ip or iv protected mice from a lethal Ebola challenge. VP35 siRNA was AD-11570

FIG. 3 is the structure of NP98 lipid.

FIG. 4 is a graph showing that siRNAs formulated with DODMA protected mice from a lethal Ebola virus challenge.

FIG. 5 is a graph showing that siRNAs formulated with DODMA were effective down to 0.04 mg/kg to protect mice injected with Ebola.

FIG. 6 is a graph showing that siRNAs formulated with DODMA were effective to protect guinea pigs from a lethal Ebola virus challenge.

FIG. 7 is a graph showing the efficacy of siRNAs against different Ebola genes formulated with DODMA in a guinea pig model of Ebola.

FIG. 8 is a graph presenting the observed decrease in viral titers in the serum of mice following administration of LNP01-formulated VP35 siRNA.

FIG. 9 shows the survival of guinea pigs treated with DODMA or LNP09 formulated siRNA or saline control.

FIG. 10 shows the weight loss of guinea pigs treated with DODMA or LNP09 formulated siRNA or saline control as measured against a percentage of the guinea pig's starting weight.

FIG. 11 shows the survival of guinea pigs treated with LNP09 formulated siRNA versus controls, administered according to the indicated dosage regimens.

FIG. 12 shows the weight loss of guinea pigs treated with LNP09 formulated siRNA versus controls, administered according to the indicated dosage regimens.

FIG. 13 shows the survival of guinea pgis treated with Formulation M formulated siRNA versus controls, administered according to the indicated dosage regimen.

FIG. 14 shows the weight loss of guinea pigs treated with Formulation M formulated siRNA versus controls, administered according to the indicated dosage regimen.

FIG. 15 shows the survival of guinea pigs treated with different lipid formulations of siRNA via different administration routes, administered according to the indicated dosage regimen.

FIG. 16 shows the weight loss of guinea pigs treated with different lipid formulations of siRNA via different administration routes, administered according to the indicated dosage regimen. The P/Q treated group includes 3 animals treated with AD-1955 E/F formulation on day 0 and AD-11570 P/Q formulation on days 1, 2, and 4.

FIG. 17 shows the survival of guinea pigs treated with different dosages of siRNA, administered according to the indicated dosage regimen.

FIG. 18 shows the weight change of guinea pigs treated with different dosages of siRNA, administered according to the indicated dosage regimen.

FIG. 19 shows the survival of guinea pigs treated with different formulations of siRNA, administered according to the indicated dosage regimen.

FIG. 20 shows the weight change of guinea pigs treated with different formulations of siRNA, administered according to the indicated dosage regimen.

FIG. 21 shows the survival of guinea pigs treated with siRNA post-Ebola challenge, administered according to the indicated dosage regimen.

FIG. 22 shows the disease index of guinea pigs treated with siRNA post-Ebola challenge, administered according to the indicated dosage regimen. 0=Healthy; no clinical signs of disease, animal active and responsive. 1=Slightly ruffled fur, reduced mobility. 2=Severely reduced mobility, hunched posture, ruffled fur, reduced responsiveness. 3=Moribund; Unresponsive, non-mobile, labored breathing. 4=Dead.

FIG. 23 shows the weight change of guinea pigs treated with siRNA post-Ebola challenge, administered according to the indicated dosage regimen.

FIG. 24 shows the viremia in guinea pigs treated with siRNA or control, administered according to the indicated dose regimen. Serum titer of Ebola virus was quantified by RT-qPCR. Treatment with AD-11570 specific siRNA in a lipid D formulation results in a dramatic suppression of Ebola virus titer.

DETAILED DESCRIPTION OF THE INVENTION

The invention provides double-stranded ribonucleic acid (dsRNA), as well as compositions and methods for inhibiting the expression of a gene from the Ebola virus in a cell or mammal using the dsRNA. The invention also provides compositions and methods for treating pathological conditions and diseases in a mammal caused by Ebola infection using dsRNA. dsRNA directs the sequence-specific degradation of mRNA through a process known as RNA interference (RNAi).

The dsRNA of the invention comprises an RNA strand (the antisense strand) having a region which is less than 30 nucleotides in length, generally 19-24 nucleotides in length, and is substantially complementary to at least part of an mRNA transcript of a gene from the Ebola virus. The use of these dsRNAs enables the targeted degradation of mRNAs of genes that are implicated in replication and or maintenance of Ebola infection and the occurance of systemic hemorrhage and multi-organ failure in a subject infected with the Ebola virus. Using cell-based and animal assays, the present inventors have demonstrated that very low dosages of these dsRNA can specifically and efficiently mediate RNAi, resulting in significant inhibition of expression of a gene from the Ebola virus. Thus, the methods and compositions of the invention comprising these dsRNAs are useful for treating pathological processes mediated by Ebolaviral infection by targeting a gene involved in Ebola relication and/or maintainance in a cell.

The following detailed description discloses how to make and use the dsRNA and compositions containing dsRNA to inhibit the expression of a gene from the Ebola virus, as well as compositions and methods for treating diseases and disorders caused by the infection with the Ebola virus, such as systemic hemorrhage and multi-organ failure. The pharmaceutical compositions of the invention comprise a dsRNA having an antisense strand comprising a region of complementarity which is less than 30 nucleotides in length, generally 19-24 nucleotides in length, and is substantially complementary to at least part of an RNA transcript of a gene from the Ebola virus, together with a pharmaceutically acceptable carrier.

Accordingly, certain aspects of the invention provide pharmaceutical compositions comprising the dsRNA of the invention together with a pharmaceutically acceptable carrier, methods of using the compositions to inhibit expression of a gene in a gene from the Ebola virus, and methods of using the pharmaceutical compositions to treat diseases caused by infection with the Ebola virus.

I. DEFINITIONS

For convenience, the meaning of certain terms and phrases used in the specification, examples, and appended claims, are provided below. If there is an apparent discrepancy between the usage of a term in other parts of this specification and its definition provided in this section, the definition in this section shall prevail.

“G,” “C,” “A” and “U” each generally stand for a nucleotide that contains guanine, cytosine, adenine, and uracil as a base, respectively. “T” and “dT” are used interchangeably herein and refer to a deoxyribonucleotide wherein the nucleobase is thymine, e.g., deoxyribothymine. However, it will be understood that the term “ribonucleotide” or “nucleotide” or “deoxyribonucleotide” can also refer to a modified nucleotide, as further detailed below, or a surrogate replacement moiety. The skilled person is well aware that guanine, cytosine, adenine, and uracil may be replaced by other moieties without substantially altering the base pairing properties of an oligonucleotide comprising a nucleotide bearing such replacement moiety. For example, without limitation, a nucleotide comprising inosine as its base may base pair with nucleotides containing adenine, cytosine, or uracil. Hence, nucleotides containing uracil, guanine, or adenine may be replaced in the nucleotide sequences of the invention by a nucleotide containing, for example, inosine. Sequences comprising such replacement moieties are embodiments of the invention.

As used herein, “Ebola viruses”, are members of the family Filoviridae, are associated with outbreaks of highly lethal hemorrhagic fever in humans and nonhuman primates. Human pathogens include Ebola Zaire, Ebola Sudan, and Ebola Ivory Coast. Ebola Reston is a monkey pathogen and is not considered a significant human pathogen. The natural reservoir of the virus is unknown and there are currently no available vaccines or effective therapeutic treatments for filovirus infections. The genome of Ebola virus consists of a single strand of negative sense RNA that is approximately 19 kb in length. This RNA contains seven sequentially arranged genes that produce 8 mRNAs upon infection. Ebola virions, like virions of other filoviruses, contain seven proteins: a surface glycoprotein (GP), a nucleoprotein (NP), four virion structural proteins (VP40, VP35, VP30, and VP24), and an RNA-dependent RNA polymerase (L) (Feldmann et al. (1992) Virus Res. 24, 1-19; Sanchez et al., (1993) Virus Res. 29, 215-240; reviewed in Peters et al. (1996) In Fields Virology, Third ed. pp. 1161-1176. Fields, B. N., Knipe, D. M., Howley, P. M., et al. eds. Lippincott-Raven Publishers, Philadelphia). The glycoprotein of Ebola virus is unusual in that it is encoded in two open reading frames. Transcriptional editing is needed to express the transmembrane form that is incorporated into the virion (Sanchez et al. (1996) Proc. Natl. Acad. Sci. USA 93, 3602-3607; Volchkov et al, (1995) Virology 214, 421-430).

As used herein, “target sequence” refers to a contiguous portion of the nucleotide sequence of an mRNA molecule formed during the transcription of a gene from the Ebola virus, including mRNA that is a product of RNA processing of a primary transcription product.

As used herein, the term “strand comprising a sequence” refers to an oligonucleotide comprising a chain of nucleotides that is described by the sequence referred to using the standard nucleotide nomenclature.

As used herein, and unless otherwise indicated, the term “complementary,” when used to describe a first nucleotide sequence in relation to a second nucleotide sequence, refers to the ability of an oligonucleotide or polynucleotide comprising the first nucleotide sequence to hybridize and form a duplex structure under certain conditions with an oligonucleotide or polynucleotide comprising the second nucleotide sequence, as will be understood by the skilled person. Such conditions can, for example, be stringent conditions, where stringent conditions may include: 400 mM NaCl, 40 mM PIPES pH 6.4, 1 mM EDTA, 50° C. or 70° C. for 12-16 hours followed by washing. Other conditions, such as physiologically relevant conditions as may be encountered inside an organism, can apply. The skilled person will be able to determine the set of conditions most appropriate for a test of complementarity of two sequences in accordance with the ultimate application of the hybridized nucleotides.

This includes base-pairing of the oligonucleotide or polynucleotide comprising the first nucleotide sequence to the oligonucleotide or polynucleotide comprising the second nucleotide sequence over the entire length of the first and second nucleotide sequence. Such sequences can be referred to as “fully complementary” with respect to each other herein. However, where a first sequence is referred to as “substantially complementary” with respect to a second sequence herein, the two sequences can be fully complementary, or they may form one or more, but generally not more than 4, 3 or 2 mismatched base pairs upon hybridization, while retaining the ability to hybridize under the conditions most relevant to their ultimate application. However, where two oligonucleotides are designed to form, upon hybridization, one or more single stranded overhangs, such overhangs shall not be regarded as mismatches with regard to the determination of complementarity. For example, a dsRNA comprising one oligonucleotide 21 nucleotides in length and another oligonucleotide 23 nucleotides in length, wherein the longer oligonucleotide comprises a sequence of 21 nucleotides that is fully complementary to the shorter oligonucleotide, may yet be referred to as “fully complementary” for the purposes of the invention.

“Complementary” sequences, as used herein, may also include, or be formed entirely from, non-Watson-Crick base pairs and/or base pairs formed from non-natural and modified nucleotides, in as far as the above requirements with respect to their ability to hybridize are fulfilled. Such non-Watson-Crick base pairs includes, but not limited to, G:U Wobble or Hoogstein base pairing.

The terms “complementary”, “fully complementary” and “substantially complementary” herein may be used with respect to the base matching between the sense strand and the antisense strand of a dsRNA, or between the antisense strand of a dsRNA and a target sequence, as will be understood from the context of their use.

As used herein, a polynucleotide which is “substantially complementary to at least part of” a messenger RNA (mRNA) refers to a polynucleotide which is substantially complementary to a contiguous portion of the mRNA of interest (e.g., encoding Ebola) including a 5′ UTR, an open reading frame (ORF), or a 3′ UTR. For example, a polynucleotide is complementary to at least a part of a Ebola mRNA if the sequence is substantially complementary to a non-interrupted portion of a mRNA encoding Ebola.

The term “double-stranded RNA” or “dsRNA,” as used herein, refers to a complex of ribonucleic acid molecules, having a duplex structure comprising two anti-parallel and substantially complementary, as defined above, nucleic acid strands. In general, the majority of nucleotides of each strand are ribonucleotides, but as described in detail herein, each or both strands can also include at least one non-ribonucleotide, e.g., a deoxyribonucleotide and/or a modified nucleotide. In addition, as used in this specification, “dsRNA” may include chemical modifications to ribonucleotides, including substantial modifications at multiple nucleotides and including all types of modifications disclosed herein or known in the art. Any such modifications, as used in an siRNA type molecule, are encompassed by “dsRNA” for the purposes of this specification and claims.

The two strands forming the duplex structure may be different portions of one larger RNA molecule, or they may be separate RNA molecules. Where the two strands are part of one larger molecule, and therefore are connected by an uninterrupted chain of nucleotides between the 3′-end of one strand and the 5′end of the respective other strand forming the duplex structure, the connecting RNA chain is referred to as a “hairpin loop”. Where the two strands are connected covalently by means other than an uninterrupted chain of nucleotides between the 3′-end of one strand and the 5′end of the respective other strand forming the duplex structure, the connecting structure is referred to as a “linker”. The RNA strands may have the same or a different number of nucleotides. The maximum number of base pairs is the number of nucleotides in the shortest strand of the dsRNA minus any overhangs that are present in the duplex. In addition to the duplex structure, a dsRNA may comprise one or more nucleotide overhangs. dsRNAs as used herein are also referred to as “siRNAs” (short interfering RNAs).

As used herein, a “nucleotide overhang” refers to the unpaired nucleotide or nucleotides that protrude from the duplex structure of a dsRNA when a 3′-end of one strand of the dsRNA extends beyond the 5′-end of the other strand, or vice versa. “Blunt” or “blunt end” means that there are no unpaired nucleotides at that end of the dsRNA, i.e., no nucleotide overhang. A “blunt ended” dsRNA is a dsRNA that is double-stranded over its entire length, i.e., no nucleotide overhang at either end of the molecule.

The term “antisense strand” refers to the strand of a dsRNA which includes a region that is substantially complementary to a target sequence. As used herein, the term “region of complementarity” refers to the region on the antisense strand that is substantially complementary to a sequence, for example a target sequence, as defined herein. Where the region of complementarity is not fully complementary to the target sequence, the mismatches are most tolerated in the terminal regions and, if present, are generally in a terminal region or regions, e.g., within 6, 5, 4, 3, or 2 nucleotides of the 5′ and/or 3′ terminus.

The term “sense strand,” as used herein, refers to the strand of a dsRNA that includes a region that is substantially complementary to a region of the antisense strand.

“Introducing into a cell”, when referring to a dsRNA, means facilitating uptake or absorption into the cell, as is understood by those skilled in the art. Absorption or uptake of dsRNA can occur through unaided diffusive or active cellular processes, or by auxiliary agents or devices. The meaning of this term is not limited to cells in vitro; a dsRNA may also be “introduced into a cell”, wherein the cell is part of a living organism. In such instance, introduction into the cell will include the delivery to the organism. For example, for in vivo delivery, dsRNA can be injected into a tissue site or administered systemically. In vitro introduction into a cell includes methods known in the art such as electroporation and lipofection.

The terms “silence,” “inhibit the expression of,” “down-regulate the expression of,” “suppress the expression of” and the like, in as far as they refer to a gene from the Ebola virus, herein refer to the at least partial suppression of the expression of a gene from the Ebola virus, as manifested by a reduction of the amount of mRNA from the Ebola virus which may be isolated from a first cell or group of cells in which a gene from the Ebola virus is transcribed and which has or have been treated such that the expression of a gene from the Ebola virus is inhibited, as compared to a second cell or group of cells substantially identical to the first cell or group of cells but which has or have not been so treated (control cells). The degree of inhibition is usually expressed in terms of

${\frac{\left( {{mRNA}\mspace{14mu} {in}\mspace{14mu} {control}\mspace{14mu} {cells}} \right) - \left( {{mRNA}\mspace{14mu} {in}\mspace{14mu} {treated}\mspace{14mu} {cells}} \right)}{\left( {{mRNA}\mspace{14mu} {in}\mspace{14mu} {control}\mspace{14mu} {cells}} \right)} \cdot 100}\%$

Alternatively, the degree of inhibition may be given in terms of a reduction of a parameter that is functionally linked to Ebola genome transcription, e.g. the amount of protein encoded by a gene from the Ebola virus, or the number of cells displaying a certain phenotype, e.g infection with the Ebola virus. In principle, Ebola genome silencing may be determined in any cell expressing the target, either constitutively or by genomic engineering, and by any appropriate assay. However, when a reference is needed in order to determine whether a given dsRNA inhibits the expression of a gene from the Ebola virus by a certain degree and therefore is encompassed by the instant invention, the assay provided in the Examples below shall serve as such reference.

For example, in certain instances, expression of a gene from the Ebola virus is suppressed by at least about 5%, 10%, 15%, 20%, 25%, 30%, 35%, 40%, 45%, or 50% by administration of the double-stranded oligonucleotide of the invention. In some embodiment, a gene from the Ebola virus is suppressed by at least about 60%, 70%, or 80% by administration of the double-stranded oligonucleotide of the invention. In some embodiments, a gene from the Ebola virus is suppressed by at least about 85%, 90%, or 95% by administration of the double-stranded oligonucleotide of the invention.

As used herein in the context of Ebola expression, the terms “treat”, “treatment”, and the like, refer to relief from or alleviation of pathological processes mediated by Ebola infection. In the context of the present invention insofar as it relates to any of the other conditions recited herein below (other than pathological processes mediated by Ebola expression), the terms “treat”, “treatment”, and the like mean to relieve or alleviate at least one symptom associated with such condition, or to slow or reverse the progression of such condition, or to reduce the amount of virus present in the infected subject.

As used herein, the phrases “therapeutically effective amount” and “prophylactically effective amount” refer to an amount that provides a therapeutic benefit in the treatment, prevention, or management of pathological processes mediated by Ebola infection or an overt symptom of pathological processes mediated by Ebola expression or the amount virus present in the patient. The specific amount that is therapeutically effective can be readily determined by ordinary medical practitioner, and may vary depending on factors known in the art, such as, e.g. the type of pathological processes mediated by Ebola infection, the patient's history and age, the stage of pathological processes mediated by Ebola infection, and the administration of other anti-pathological processes mediated by Ebola infection.

As used herein, a “pharmaceutical composition” comprises a pharmacologically effective amount of a dsRNA and a pharmaceutically acceptable carrier. As used herein, “pharmacologically effective amount,” “therapeutically effective amount” or simply “effective amount” refers to that amount of an RNA effective to produce the intended pharmacological, therapeutic or preventive result. For example, if a given clinical treatment is considered effective when there is at least a 25% reduction in a measurable parameter associated with a disease or disorder, a therapeutically effective amount of a drug for the treatment of that disease or disorder is the amount necessary to effect at least a 25% reduction in that parameter. Further, the pharmaceutical composition can be designed to enhance targeting cells involved in Ebola infection such as dendritic cells, macrophages, hepatocytes, and other parenchymal cells.

The term “pharmaceutically acceptable carrier” refers to a carrier for administration of a therapeutic agent. Such carriers include, but are not limited to, saline, buffered saline, dextrose, water, glycerol, ethanol, and combinations thereof. The term specifically excludes cell culture medium. For drugs administered orally, pharmaceutically acceptable carriers include, but are not limited to pharmaceutically acceptable excipients such as inert diluents, disintegrating agents, binding agents, lubricating agents, sweetening agents, flavoring agents, coloring agents and preservatives. Suitable inert diluents include sodium and calcium carbonate, sodium and calcium phosphate, and lactose, while corn starch and alginic acid are suitable disintegrating agents. Binding agents may include starch and gelatin, while the lubricating agent, if present, will generally be magnesium stearate, stearic acid or talc. If desired, the tablets may be coated with a material such as glyceryl monostearate or glyceryl distearate, to delay absorption in the gastrointestinal tract.

As used herein, a “transformed cell” is a cell into which a vector has been introduced from which a dsRNA molecule may be expressed.

II. DOUBLE-STRANDED RIBONUCLEIC ACID (DSRNA)

As described in more detail herein, the invention provides double-stranded ribonucleic acid (dsRNA) molecules for inhibiting the expression of a gene from the Ebola virus in a cell or mammal, wherein the dsRNA comprises an antisense strand comprising a region of complementarity which is complementary to at least a part of an mRNA formed in the expression of a gene from the Ebola virus, and wherein the region of complementarity is less than 30 nucleotides in length, generally 19-24 nucleotides in length, and wherein said dsRNA, upon contact with a cell expressing the gene from the Ebola virus, inhibits the expression of the Ebola virus gene by at least 40%. The dsRNA of the invention can further include one or more single-stranded nucleotide overhangs.

The dsRNA can be synthesized by standard methods known in the art as further discussed below, e.g., by use of an automated DNA synthesizer, such as are commercially available from, for example, Biosearch, Applied Biosystems, Inc. The dsRNA comprises two RNA strands that are sufficiently complementary to hybridize to form a duplex structure. One strand of the dsRNA (the antisense strand) comprises a region of complementarity that is substantially complementary, and generally fully complementary, to a target sequence, derived from the sequence of an mRNA formed during the expression of a gene from the Ebola virus, the other strand (the sense strand) comprises a region which is complementary to the antisense strand, such that the two strands hybridize and form a duplex structure when combined under suitable conditions. Generally, the duplex structure is between 15 and 30, or between 25 and 30, or between 18 and 25, or between 19 and 24, or between 19 and 21, or 19, 20, or 21 base pairs in length. In one embodiment the duplex is 19 base pairs in length. In another embodiment the duplex is 21 base pairs in length. When two different siRNAs are used in combination, the duplex lengths can be identical or can differ.

Each strand of the dsRNA of invention is generally between 15 and 30, or between 18 and 25, or 18, 19, 20, 21, 22, 23, 24, or 25 nucleotides in length. In other embodiments, each is strand is 25-30 nucleotides in length. Each strand of the duplex can be the same length or of different lengths. When two different siRNAs are used in combination, the lengths of each strand of each siRNA can be identical or can differ.

The dsRNA of the invention can include one or more single-stranded overhang(s) of one or more nucleotides. In one embodiment, at least one end of the dsRNA has a single-stranded nucleotide overhang of 1 to 4, generally 1 or 2 nucleotides. In another embodiment, the antisense strand of the dsRNA has 1-10 nucleotides overhangs each at the 3′ end and the 5′ end over the sense strand. In further embodiments, the sense strand of the dsRNA has 1-10 nucleotides overhangs each at the 3′ end and the 5′ end over the antisense strand.

A dsRNAs having at least one nucleotide overhang can have unexpectedly superior inhibitory properties than the blunt-ended counterpart. In some embodiments the presence of only one nucleotide overhang strengthens the interference activity of the dsRNA, without affecting its overall stability. A dsRNA having only one overhang has proven particularly stable and effective in vivo, as well as in a variety of cells, cell culture mediums, blood, and serum. Generally, the single-stranded overhang is located at the 3′-terminal end of the antisense strand or, alternatively, at the 3′-terminal end of the sense strand. The dsRNA can also have a blunt end, generally located at the 5′-end of the antisense strand. Such dsRNAs can have improved stability and inhibitory activity, thus allowing administration at low dosages, i.e., less than 5 mg/kg body weight of the recipient per day. Generally, the antisense strand of the dsRNA has a nucleotide overhang at the 3′-end, and the 5′-end is blunt. In another embodiment, one or more of the nucleotides in the overhang is replaced with a nucleoside thiophosphate.

In one embodiment, a gene from the Ebola virus is the from human Ebola genome. In specific embodiments, the sense strand of the dsRNA is one of the sense sequences of Table 2 or Table 5 and the antisense strand is one of the antisense sequences of Table 2 or Table 5. Alternative antisense agents that target elsewhere in the target sequences provided in Table 2 or Table 5 can readily be determined using the target sequence and the flanking Ebola sequence.

The skilled person is well aware that dsRNAs comprising a duplex structure of between 20 and 23, but specifically 21, base pairs have been hailed as particularly effective in inducing RNA interference (Elbashir et al., EMBO 2001, 20:6877-6888). However, others have found that shorter or longer dsRNAs can be effective as well. In the embodiments described above, by virtue of the nature of the oligonucleotide sequences provided in Table 2 or Table 5, the dsRNAs of the invention can comprise at least one strand of a length of described therein. It can be reasonably expected that shorter dsRNAs comprising one of the sequences of Table 2 or Table 5 minus only a few nucleotides on one or both ends may be similarly effective as compared to the dsRNAs described above. Hence, dsRNAs comprising a partial sequence of at least 15, 16, 17, 18, 19, 20, 21, or 22 or more contiguous nucleotides from one of the sequences of Table 2 or Table 5, and differing in their ability to inhibit the expression of a gene from the Ebola virus in an assay as described herein below by not more than 5, 10, 15, 20, 25, or 30% inhibition from a dsRNA comprising the full sequence, are contemplated by the invention. Further dsRNAs that cleave within the target sequence provided in Table 2 or Table 5 can readily be made using the Ebola virus sequence and the target sequence provided.

In addition, the dsRNA agents provided in Table 2 or Table 5 identify a site in the Ebola virus mRNA that is susceptible to RNAi based cleavage. As such the present invention further includes dsRNA agents that target within the sequence targeted by one of the agents of the present invention. As used herein a second dsRNA agent is said to target within the sequence of a first or Table 5agent if the second or Table 5agent cleaves the message anywhere within the mRNA that is complementary to the antisense strand of the first or Table 5agent. Such a second agent will generally consist of at least 15 contiguous nucleotides from one of the sequences provided in Table 2 or Table 5 coupled to additional nucleotide sequences taken from the region contiguous to the selected sequence in a gene from the Ebola virus. For example, the last 15 nucleotides of SEQ ID NO:1 combined with the next 6 nucleotides from the target Ebola genome produces a single strand agent of 21 nucleotides that is based on one of the sequences provided in Table 2.

The dsRNA of the invention can contain one or more mismatches to the target sequence. In one embodiment, the dsRNA of the invention contains no more than 3 mismatches. If the antisense strand of the dsRNA contains mismatches to a target sequence, it is preferable that the area of mismatch not be located in the center of the region of complementarity. If the antisense strand of the dsRNA contains mismatches to the target sequence, it is preferable that the mismatch be restricted to 5 nucleotides from either end, for example 5, 4, 3, 2, or 1 nucleotide from either the 5′ or 3′ end of the region of complementarity. For example, for a 23 nucleotide dsRNA strand which is complementary to a region of a gene from the Ebola virus, the dsRNA generally does not contain any mismatch within the central 13 nucleotides. The methods described within the invention can be used to determine whether a dsRNA containing a mismatch to a target sequence is effective in inhibiting the expression of a gene from the Ebola virus. Consideration of the efficacy of dsRNAs with mismatches in inhibiting expression of a gene from the Ebola virus is important, especially if the particular region of complementarity in a gene from the Ebola virus is known to have polymorphic sequence variation within the population.

Modifications

In yet another embodiment, the dsRNA is chemically modified to enhance stability. The nucleic acids of the invention may be synthesized and/or modified by methods well established in the art, such as those described in “Current protocols in nucleic acid chemistry”, Beaucage, S. L. et al. (Edrs.), John Wiley & Sons, Inc., New York, N.Y., USA, which is hereby incorporated herein by reference. Specific examples of dsRNA compounds useful in this invention include dsRNAs containing modified backbones or no natural internucleoside linkages. As defined in this specification, dsRNAs having modified backbones include those that retain a phosphorus atom in the backbone and those that do not have a phosphorus atom in the backbone. For the purposes of this specification, and as sometimes referenced in the art, modified dsRNAs that do not have a phosphorus atom in their internucleoside backbone can also be considered to be oligonucleosides.

Preferred modified dsRNA backbones include, for example, phosphorothioates, chiral phosphorothioates, phosphorodithioates, phosphotriesters, aminoalkylphosphotriesters, methyl and other alkyl phosphonates including 3′-alkylene phosphonates and chiral phosphonates, phosphinates, phosphoramidates including 3′-amino phosphoramidate and aminoalkylphosphoramidates, thionophosphoramidates, thionoalkylphosphonates, thionoalkylphosphotriesters, and boranophosphates having normal 3′-5′ linkages, 2′-5′ linked analogs of these, and those) having inverted polarity wherein the adjacent pairs of nucleoside units are linked 3′-5′ to 5′-3′ or 2′-5′ to 5′-2′. Various salts, mixed salts and free acid forms are also included.

Representative U.S. patents that teach the preparation of the above phosphorus-containing linkages include, but are not limited to, U.S. Pat. Nos. 3,687,808; 4,469,863; 4,476,301; 5,023,243; 5,177,195; 5,188,897; 5,264,423; 5,276,019; 5,278,302; 5,286,717; 5,321,131; 5,399,676; 5,405,939; 5,453,496; 5,455,233; 5,466,677; 5,476,925; 5,519,126; 5,536,821; 5,541,316; 5,550,111; 5,563,253; 5,571,799; 5,587,361; and 5,625,050, each of which is herein incorporated by reference

Preferred modified dsRNA backbones that do not include a phosphorus atom therein have backbones that are formed by short chain alkyl or cycloalkyl internucleoside linkages, mixed heteroatoms and alkyl or cycloalkyl internucleoside linkages, or ore or more short chain heteroatomic or heterocyclic internucleoside linkages. These include those having morpholino linkages (formed in part from the sugar portion of a nucleoside); siloxane backbones; sulfide, sulfoxide and sulfone backbones; formacetyl and thioformacetyl backbones; methylene formacetyl and thioformacetyl backbones; alkene containing backbones; sulfamate backbones; methyleneimino and methylenehydrazino backbones; sulfonate and sulfonamide backbones; amide backbones; and others having mixed N, O, S and CH2 component parts.

Representative U.S. patents that teach the preparation of the above oligonucleosides include, but are not limited to, U.S. Pat. Nos. 5,034,506; 5,166,315; 5,185,444; 5,214,134; 5,216,141; 5,235,033; 5,64,562; 5,264,564; 5,405,938; 5,434,257; 5,466,677; 5,470,967; 5,489,677; 5,541,307; 5,561,225; 5,596,086; 5,602,240; 5,608,046; 5,610,289; 5,618,704; 5,623,070; 5,663,312; 5,633,360; 5,677,437; and, 5,677,439, each of which is herein incorporated by reference.

In other certain dsRNA mimetics, both the sugar and the internucleoside linkage, i.e., the backbone, of the nucleotide units are replaced with novel groups. The base units are maintained for hybridization with an appropriate nucleic acid target compound. One such oligomeric compound, an dsRNA mimetic that has been shown to have excellent hybridization properties, is referred to as a peptide nucleic acid (PNA). In PNA compounds, the sugar backbone of an dsRNA is replaced with an amide containing backbone, in particular an aminoethylglycine backbone. The nucleobases are retained and are bound directly or indirectly to aza nitrogen atoms of the amide portion of the backbone. Representative U.S. patents that teach the preparation of PNA compounds include, but are not limited to, U.S. Pat. Nos. 5,539,082; 5,714,331; and 5,719,262, each of which is herein incorporated by reference. Further teaching of PNA compounds can be found in Nielsen et al., Science, 1991, 254, 1497-1500.

Other embodiments of the invention are dsRNAs with phosphorothioate backbones and oligonucleosides with heteroatom backbones, and in particular —CH₂—NH—CH₂—, —CH₂—N(CH₃)—O—CH₂— [known as a methylene (methylimino) or MMI backbone], —CH₂—O—N(CH₃)—CH₂—, —CH₂—N(CH₃)—N(CH₃)—CH₂— and —N(CH₃)—CH₂—CH₂— [wherein the native phosphodiester backbone is represented as —O—P—O—CH₂—] of the above-referenced U.S. Pat. No. 5,489,677, and the amide backbones of the above-referenced U.S. Pat. No. 5,602,240. Also preferred are dsRNAs having morpholino backbone structures of the above-referenced U.S. Pat. No. 5,034,506.

Modified dsRNAs may also contain one or more substituted sugar moieties. Preferred dsRNAs comprise one of the following at the 2′ position: OH; F; O-, S-, or N-alkyl; O-, S-, or N-alkenyl; O-, S- or N-alkynyl; or O-alkyl-O-alkyl, wherein the alkyl, alkenyl and alkynyl may be substituted or unsubstituted C₁ to C₁₀ alkyl or C₂ to C₁₀ alkenyl and alkynyl. Particularly preferred are O[(CH₂)_(n)O]_(m)CH₃, O(CH₂)_(n)OCH₃, O(CH₂)_(n)NH₂, O(CH₂)_(n)CH₃, O(CH₂)_(n)ONH₂, and O(CH₂)_(n)ON[(CH₂)_(n)CH₃)]₂, where n and m are from 1 to about 10. Other preferred dsRNAs comprise one of the following at the 2′ position: C₁ to C₁₀ lower alkyl, substituted lower alkyl, alkaryl, aralkyl, O-alkaryl or O-aralkyl, SH, SCH₃, OCN, Cl, Br, CN, CF₃, OCF₃, SOCH₃, SO₂CH₃, ONO₂, NO₂, N₃, NH₂, heterocycloalkyl, heterocycloalkaryl, aminoalkylamino, polyalkylamino, substituted silyl, an RNA cleaving group, a reporter group, an intercalator, a group for improving the pharmacokinetic properties of an dsRNA, or a group for improving the pharmacodynamic properties of an dsRNA, and other substituents having similar properties. A preferred modification includes 2′-methoxyethoxy (2′-O—CH₂CH₂OCH₃, also known as 2′-O-(2-methoxyethyl) or 2′-MOE) (Martin et al., Helv. Chim. Acta, 1995, 78, 486-504) i.e., an alkoxy-alkoxy group. A further preferred modification includes 2′-dimethylaminooxyethoxy, i.e., a O(CH₂)₂ON(CH₃)₂ group, also known as 2′-DMAOE, as described in examples herein below, and 2′-dimethylaminoethoxyethoxy (also known in the art as 2′-O-dimethylaminoethoxyethyl or 2′-DMAEOE), i.e., 2′-O—CH₂—O—CH₂—N(CH₂)₂, also described in examples herein below.

Other preferred modifications include 2′-methoxy (2′-OCH₃), 2′-aminopropoxy (2′-OCH₂CH₂CH₂NH₂) and 2′-fluoro (2′-F). Similar modifications may also be made at other positions on the dsRNA, particularly the 3′ position of the sugar on the 3′ terminal nucleotide or in 2′-5′ linked dsRNAs and the 5′ position of 5′ terminal nucleotide. DsRNAs may also have sugar mimetics such as cyclobutyl moieties in place of the pentofuranosyl sugar. Representative U.S. patents that teach the preparation of such modified sugar structures include, but are not limited to, U.S. Pat. Nos. 4,981,957; 5,118,800; 5,319,080; 5,359,044; 5,393,878; 5,446,137; 5,466,786; 5,514,785; 5,519,134; 5,567,811; 5,576,427; 5,591,722; 5,597,909; 5,610,300; 5,627,053; 5,639,873; 5,646,265; 5,658,873; 5,670,633; and 5,700,920, certain of which are commonly owned with the instant application, and each of which is herein incorporated by reference in its entirety.

dsRNAs may also include nucleobase (often referred to in the art simply as “base”) modifications or substitutions. As used herein, “unmodified” or “natural” nucleobases include the purine bases adenine (A) and guanine (G), and the pyrimidine bases thymine (T), cytosine (C) and uracil (U). Modified nucleobases include other synthetic and natural nucleobases such as 5-methylcytosine (5-me-C), 5-hydroxymethyl cytosine, xanthine, hypoxanthine, 2-aminoadenine, 6-methyl and other alkyl derivatives of adenine and guanine, 2-propyl and other alkyl derivatives of adenine and guanine, 2-thiouracil, 2-thiothymine and 2-thiocytosine, 5-halouracil and cytosine, 5-propynyl uracil and cytosine, 6-azo uracil, cytosine and thymine, 5-uracil (pseudouracil), 4-thiouracil, 8-halo, 8-amino, 8-thiol, 8-thioalkyl, 8-hydroxyl anal other 8-substituted adenines and guanines, 5-halo, particularly 5-bromo, 5-trifluoromethyl and other 5-substituted uracils and cytosines, 7-methylguanine and 7-methyladenine, 8-azaguanine and 8-azaadenine, 7-deazaguanine and 7-daazaadenine and 3-deazaguanine and 3-deazaadenine. Further nucleobases include those disclosed in U.S. Pat. No. 3,687,808, those disclosed in The Concise Encyclopedia Of Polymer Science And Engineering, pages 858-859, Kroschwitz, J. L, ed. John Wiley & Sons, 1990, these disclosed by Englisch et al., Angewandte Chemie, International Edition, 1991, 30, 613, and those disclosed by Sanghvi, Y S., Chapter 15, DsRNA Research and Applications, pages 289-302, Crooke, S. T. and Lebleu, B., Ed., CRC Press, 1993. Certain of these nucleobases are particularly useful for increasing the binding affinity of the oligomeric compounds of the invention. These include 5-substituted pyrimidines, 6-azapyrimidines and N-2, N-6 and 0-6 substituted purines, including 2-aminopropyladenine, 5-propynyluracil and 5-propynylcytosine. 5-methyl cytosine substitutions have been shown to increase nucleic acid duplex stability by 0.6-1.2.degree. C. (Sanghvi, Y. S., Crooke, S. T. and Lebleu, B., Eds., DsRNA Research and Applications, CRC Press, Boca Raton, 1993, pp. 276-278) and are presently preferred base substitutions, even more particularly when combined with 2′-O-methoxyethyl sugar modifications.

Other nucleotide substitutions, such as “Universal” bases can be incorporated into siRNA duplexes to increase the number of target sequences (or in this case, number of different Ebola strains) any particular siRNA might have complementarity to and activity against. Universal bases are non-canonical synthetic molecules that mimic structures of traditional nucleotides (the genetic building blocks of DNA and RNA). However, instead of selectively pairing according to Watson/Crick rules (A with T or U, C with G), universal bases ‘stack’ equally well with all natural bases. Incorporating universal bases into siRNAs may enable the siRNA to tolerate a mutation at that specific site in its target mRNA. Thus, by decreasing the need for absolute complementarity between siRNA and its mRNA target, universal-base containing siRNAs may be an approach to (1) prevent drug resistance caused by site-specific viral mutations and (2) create siRNAs able to be broadly reactive across viral species with similar, but not absolutely conserved, targets. Among the modifications that can be used as universal basacs are: 3-Nitropyrrole, 5-Nitroindole, Imidazole-4-Carboxamide, 2,4-difluorotoluyl, and Inosine.

Representative U.S. patents that teach the preparation of certain of the above noted modified nucleobases as well as other modified nucleobases include, but are not limited to, the above noted U.S. Pat. No. 3,687,808, as well as U.S. Pat. Nos. 4,845,205; 5,130,30; 5,134,066; 5,175,273; 5,367,066; 5,432,272; 5,457,187; 5,459,255; 5,484,908; 5,502,177; 5,525,711; 5,552,540; 5,587,469; 5,594,121, 5,596,091; 5,614,617; and 5,681,941, each of which is herein incorporated by reference, and U.S. Pat. No. 5,750,692, also herein incorporated by reference.

Conjugates

Another modification of the dsRNAs of the invention involves chemically linking to the dsRNA one or more moieties or conjugates which enhance the activity, cellular distribution or cellular uptake of the dsRNA. Such moieties include but are not limited to lipid moieties such as a cholesterol moiety (Letsinger et al., Proc. Natl. Acid. Sci. USA, 199, 86, 6553-6556), cholic acid (Manoharan et al., Biorg. Med. Chem. Let., 1994 4 1053-1060), a thioether, e.g., beryl-S-tritylthiol (Manoharan et al., Ann. N.Y. Acad. Sci., 1992, 660, 306-309; Manoharan et al., Biorg. Med. Chem. Let., 1993, 3, 2765-2770), a thiocholesterol (Oberhauser et al., Nucl. Acids Res., 1992, 20, 533-538), an aliphatic chain, e.g., dodecandiol or undecyl residues (Saison-Behmoaras et al., EMBO J, 1991, 10, 1111-1118; Kabanov et al., FEBS Lett., 1990, 259, 327-330; Svinarchuk et al., Biochimic, 1993, 75, 49-54), a phospholipid, e.g., di-hexadecyl-rac-glycerol or triethyl-ammonium 1,2-di-O-hexadecyl-rac-glycero-3-Hphosphonate (Manoharan et al., Tetrahedron Lett., 1995, 36, 3651-3654; Shea et al., Nucl. Acids Res., 1990, 18, 3777-3783), a polyamine or a polyethylene glycol chain (Manoharan et al., Nucleosides & Nucleotides, 1995, 14, 969-973), or adamantane acetic acid (Manoharan et al., Tetrahedron Lett., 1995, 36, 3651-3654), a palmityl moiety (Mishra et al., Biochim. Biophys. Acta, 1995, 1264, 229-237), or an octadecylamine or hexylamino-carbonyloxycholesterol moiety (Crooke et al., J. Pharmacol. Exp. Ther., 1996, 277, 923-937). Preferred conjugates will assist in targeting cells infected by Ebola virus such as dendritic cells and macrophages which are involved in early stages of infection and hepatocytes and other parenchymal cells which are involved in later phases of the infection. Such conjugates include, but are not limited to, mannose and folate conjugates.

Representative U.S. patents that teach the preparation of such dsRNA conjugates include, but are not limited to, U.S. Pat. Nos. 4,828,979; 4,948,882; 5,218,105; 5,525,465; 5,541,313; 5,545,730; 5,552,538; 5,578,717, 5,580,731; 5,591,584; 5,109,124; 5,118,802; 5,138,045; 5,414,077; 5,486,603; 5,512,439; 5,578,718; 5,608,046; 4,587,044; 4,605,735; 4,667,025; 4,762,779; 4,789,737; 4,824,941; 4,835,263; 4,876,335; 4,904,582; 4,958,013; 5,082,830; 5,112,963; 5,214,136; 5,082,830; 5,112,963; 5,214,136; 5,245,022; 5,254,469; 5,258,506; 5,262,536; 5,272,250; 5,292,873; 5,317,098; 5,371,241, 5,391,723; 5,416,203, 5,451,463; 5,510,475; 5,512,667; 5,514,785; 5,565,552; 5,567,810; 5,574,142; 5,585,481; 5,587,371; 5,595,726; 5,597,696; 5,599,923; 5,599,928 and 5,688,941, each of which is herein incorporated by reference.

It is not necessary for all positions in a given compound to be uniformly modified, and in fact more than one of the aforementioned modifications may be incorporated in a single compound or even at a single nucleoside within an dsRNA. The present invention also includes dsRNA compounds which are chimeric compounds. “Chimeric” dsRNA compounds or “chimeras,” in the context of this invention, are dsRNA compounds, particularly dsRNAs, which contain two or more chemically distinct regions, each made up of at least one monomer unit, i.e., a nucleotide in the case of an dsRNA compound. These dsRNAs typically contain at least one region wherein the dsRNA is modified so as to confer upon the dsRNA increased resistance to nuclease degradation, increased cellular uptake, and/or increased binding affinity for the target nucleic acid. An additional region of the dsRNA may serve as a substrate for enzymes capable of cleaving RNA:DNA or RNA:RNA hybrids. By way of example, RNase H is a cellular endonuclease which cleaves the RNA strand of an RNA:DNA duplex. Activation of RNase H, therefore, results in cleavage of the RNA target, thereby greatly enhancing the efficiency of dsRNA inhibition of gene expression. Consequently, comparable results can often be obtained with shorter dsRNAs when chimeric dsRNAs are used, compared to phosphorothioate deoxydsRNAs hybridizing to the same target region. Cleavage of the RNA target can be routinely detected by gel electrophoresis and, if necessary, associated nucleic acid hybridization techniques known in the art.

In certain instances, the dsRNA may be modified by a non-ligand group. A number of non-ligand molecules have been conjugated to dsRNAs in order to enhance the activity, cellular distribution or cellular uptake of the dsRNA, and procedures for performing such conjugations are available in the scientific literature. Such non-ligand moieties have included lipid moieties, such as cholesterol (Letsinger et al., Proc. Natl. Acad. Sci. USA, 1989, 86:6553), cholic acid (Manoharan et al., Bioorg. Med. Chem. Lett., 1994, 4:1053), a thioether, e.g., hexyl-S-tritylthiol (Manoharan et al., Ann N.Y. Acad. Sci., 1992, 660:306; Manoharan et al., Bioorg. Med. Chem. Let., 1993, 3:2765), a thiocholesterol (Oberhauser et al., Nucl. Acids Res., 1992, 20:533), an aliphatic chain, e.g., dodecandiol or undecyl residues (Saison-Behmoaras et al., EMBO J., 1991, 10:111; Kabanov et al., FEBS Lett., 1990, 259:327; Svinarchuk et al., Biochimie, 1993, 75:49), a phospholipid, e.g., di-hexadecyl-rac-glycerol or triethylammonium 1,2-di-O-hexadecyl-rac-glycero-3-H-phosphonate (Manoharan et al., Tetrahedron Lett., 1995, 36:3651; Shea et al., Nucl. Acids Res., 1990, 18:3777), a polyamine or a polyethylene glycol chain (Manoharan et al., Nucleosides & Nucleotides, 1995, 14:969), or adamantane acetic acid (Manoharan et al., Tetrahedron Lett., 1995, 36:3651), a palmityl moiety (Mishra et al., Biochim. Biophys. Acta, 1995, 1264:229), or an octadecylamine or hexylamino-carbonyl-oxycholesterol moiety (Crooke et al., J. Pharmacol. Exp. Ther., 1996, 277:923). Representative United States patents that teach the preparation of such dsRNA conjugates have been listed above. Typical conjugation protocols involve the synthesis of dsRNAs bearing an aminolinker at one or more positions of the sequence. The amino group is then reacted with the molecule being conjugated using appropriate coupling or activating reagents. The conjugation reaction may be performed either with the dsRNA still bound to the solid support or following cleavage of the dsRNA in solution phase. Purification of the dsRNA conjugate by HPLC typically affords the pure conjugate.

Synthesis

Teachings regarding the synthesis of particular modified oligonucleotides may be found in the following U.S. patents: U.S. Pat. Nos. 5,138,045 and 5,218,105, drawn to polyamine conjugated oligonucleotides; U.S. Pat. No. 5,212,295, drawn to monomers for the preparation of oligonucleotides having chiral phosphorus linkages; U.S. Pat. Nos. 5,378,825 and 5,541,307, drawn to oligonucleotides having modified backbones; U.S. Pat. No. 5,386,023, drawn to backbone-modified oligonucleotides and the preparation thereof through reductive coupling; U.S. Pat. No. 5,457,191, drawn to modified nucleobases based on the 3-deazapurine ring system and methods of synthesis thereof; U.S. Pat. No. 5,459,255, drawn to modified nucleobases based on N-2 substituted purines; U.S. Pat. No. 5,521,302, drawn to processes for preparing oligonucleotides having chiral phosphorus linkages; U.S. Pat. No. 5,539,082, drawn to peptide nucleic acids; U.S. Pat. No. 5,554,746, drawn to oligonucleotides having β-lactam backbones; U.S. Pat. No. 5,571,902, drawn to methods and materials for the synthesis of oligonucleotides; U.S. Pat. No. 5,578,718, drawn to nucleosides having alkylthio groups, wherein such groups may be used as linkers to other moieties attached at any of a variety of positions of the nucleoside; U.S. Pat. Nos. 5,587,361 and 5,599,797, drawn to oligonucleotides having phosphorothioate linkages of high chiral purity; U.S. Pat. No. 5,506,351, drawn to processes for the preparation of 2′-O-alkyl guanosine and related compounds, including 2,6-diaminopurine compounds; U.S. Pat. No. 5,587,469, drawn to oligonucleotides having N-2 substituted purines; U.S. Pat. No. 5,587,470, drawn to oligonucleotides having 3-deazapurines; U.S. Pat. No. 5,223,168, and U.S. Pat. No. 5,608,046, both drawn to conjugated 4′-desmethyl nucleoside analogs; U.S. Pat. Nos. 5,602,240, and 5,610,289, drawn to backbone-modified oligonucleotide analogs; U.S. Pat. Nos. 6,262,241, and 5,459,255, drawn to, inter alia, methods of synthesizing 2′-fluoro-oligonucleotides.

In the ligand-conjugated dsRNA and ligand-molecule bearing sequence-specific linked nucleosides of the invention, the oligonucleotides and oligonucleosides may be assembled on a suitable DNA synthesizer utilizing standard nucleotide or nucleoside precursors, or nucleotide or nucleoside conjugate precursors that already bear the linking moiety, ligand-nucleotide or nucleoside-conjugate precursors that already bear the ligand molecule, or non-nucleoside ligand-bearing building blocks.

When using nucleotide-conjugate precursors that already bear a linking moiety, the synthesis of the sequence-specific linked nucleosides is typically completed, and the ligand molecule is then reacted with the linking moiety to form the ligand-conjugated oligonucleotide. Oligonucleotide conjugates bearing a variety of molecules such as steroids, vitamins, lipids and reporter molecules, has previously been described (see Manoharan et al., PCT Application WO 93/07883). In one embodiment, the oligonucleotides or linked nucleosides featured in the invention are synthesized by an automated synthesizer using phosphoramidites derived from ligand-nucleoside conjugates in addition to the standard phosphoramidites and non-standard phosphoramidites that are commercially available and routinely used in oligonucleotide synthesis.

The incorporation of a 2′-O-methyl, 2′-O-ethyl, 2′-O-propyl, 2′-O-allyl, 2′-O-aminoalkyl or 2′-deoxy-2′-fluoro group in nucleosides of an oligonucleotide confers enhanced hybridization properties to the oligonucleotide. Further, oligonucleotides containing phosphorothioate backbones have enhanced nuclease stability. Thus, functionalized, linked nucleosides of the invention can be augmented to include either or both a phosphorothioate backbone or a 2′-O-methyl, 2′-O-ethyl, 2′-O-propyl, 2′-O-aminoalkyl, 2′-O-allyl or 2′-deoxy-2′-fluoro group. A summary listing of some of the oligonucleotide modifications known in the art is found at, for example, PCT Publication WO 200370918.

In some embodiments, functionalized nucleoside sequences of the invention possessing an amino group at the 5′-terminus are prepared using a DNA synthesizer, and then reacted with an active ester derivative of a selected ligand. Active ester derivatives are well known to those skilled in the art. Representative active esters include N-hydrosuccinimide esters, tetrafluorophenolic esters, pentafluorophenolic esters and pentachlorophenolic esters. The reaction of the amino group and the active ester produces an oligonucleotide in which the selected ligand is attached to the 5′-position through a linking group. The amino group at the 5′-terminus can be prepared utilizing a 5′-Amino-Modifier C6 reagent. In one embodiment, ligand molecules may be conjugated to oligonucleotides at the 5′-position by the use of a ligand-nucleoside phosphoramidite wherein the ligand is linked to the 5′-hydroxy group directly or indirectly via a linker. Such ligand-nucleoside phosphoramidites are typically used at the end of an automated synthesis procedure to provide a ligand-conjugated oligonucleotide bearing the ligand at the 5′-terminus.

Examples of modified internucleoside linkages or backbones include, for example, phosphorothioates, chiral phosphorothioates, phosphorodithioates, phosphotriesters, aminoalkylphosphotriesters, methyl and other alkyl phosphonates including 3′-alkylene phosphonates and chiral phosphonates, phosphinates, phosphoramidates including 3′-amino phosphoramidate and aminoalkylphosphoramidates, thionophosphoramidates, thionoalkylphosphonates, thionoalkylphosphotriesters, and boranophosphates having normal 3′-5′ linkages, 2′-5′ linked analogs of these, and those having inverted polarity wherein the adjacent pairs of nucleoside units are linked 3′-5′ to 5′-3′ or 2′-5′ to 5′-2′. Various salts, mixed salts and free-acid forms are also included.

Representative United States Patents relating to the preparation of the above phosphorus-atom-containing linkages include, but are not limited to, U.S. Pat. Nos. 3,687,808; 4,469,863; 4,476,301; 5,023,243; 5,177,196; 5,188,897; 5,264,423; 5,276,019; 5,278,302; 5,286,717; 5,321,131; 5,399,676; 5,405,939; 5,453,496; 5,455,233; 5,466,677; 5,476,925; 5,519,126; 5,536,821; 5,541,306; 5,550,111; 5,563,253; 5,571,799; 5,587,361; 5,625,050; and 5,697,248, each of which is herein incorporated by reference.

Examples of modified internucleoside linkages or backbones that do not include a phosphorus atom therein (i.e., oligonucleosides) have backbones that are formed by short chain alkyl or cycloalkyl intersugar linkages, mixed heteroatom and alkyl or cycloalkyl intersugar linkages, or one or more short chain heteroatomic or heterocyclic intersugar linkages. These include those having morpholino linkages (formed in part from the sugar portion of a nucleoside); siloxane backbones; sulfide, sulfoxide and sulfone backbones; formacetyl and thioformacetyl backbones; methylene formacetyl and thioformacetyl backbones; alkene containing backbones; sulfamate backbones; methyleneimino and methylenehydrazino backbones; sulfonate and sulfonamide backbones; amide backbones; and others having mixed N, O, S and CH₂ component parts.

Representative United States patents relating to the preparation of the above oligonucleosides include, but are not limited to, U.S. Pat. Nos. 5,034,506; 5,166,315; 5,185,444; 5,214,134; 5,216,141; 5,235,033; 5,264,562; 5,264,564; 5,405,938; 5,434,257; 5,466,677; 5,470,967; 5,489,677; 5,541,307; 5,561,225; 5,596,086; 5,602,240; 5,610,289; 5,602,240; 5,608,046; 5,610,289; 5,618,704; 5,623,070; 5,663,312; 5,633,360; 5,677,437; and 5,677,439, each of which is herein incorporated by reference.

In certain instances, the oligonucleotide may be modified by a non-ligand group. A number of non-ligand molecules have been conjugated to oligonucleotides in order to enhance the activity, cellular distribution or cellular uptake of the oligonucleotide, and procedures for performing such conjugations are available in the scientific literature. Such non-ligand moieties have included lipid moieties, such as cholesterol (Letsinger et al., Proc. Natl. Acad. Sci. USA, 1989, 86:6553), cholic acid (Manoharan et al., Bioorg. Med. Chem. Lett., 1994, 4:1053), a thioether, e.g., hexyl-S-tritylthiol (Manoharan et al., Ann. N.Y. Acad. Sci., 1992, 660:306; Manoharan et al., Bioorg. Med. Chem. Let., 1993, 3:2765), a thiocholesterol (Oberhauser et al., Nucl. Acids Res., 1992, 20:533), an aliphatic chain, e.g., dodecandiol or undecyl residues (Saison-Behmoaras et al., EMBO J., 1991, 10:111; Kabanov et al., FEBS Lett., 1990, 259:327; Svinarchuk et al., Biochimie, 1993, 75:49), a phospholipid, e.g., di-hexadecyl-rac-glycerol or triethylammonium 1,2-di-O-hexadecyl-rac-glycero-3-H-phosphonate (Manoharan et al., Tetrahedron Lett., 1995, 36:3651; Shea et al., Nucl. Acids Res., 1990, 18:3777), a polyamine or a polyethylene glycol chain (Manoharan et al., Nucleosides & Nucleotides, 1995, 14:969), or adamantane acetic acid (Manoharan et al., Tetrahedron Lett., 1995, 36:3651), a palmityl moiety (Mishra et al., Biochim. Biophys. Acta, 1995, 1264:229), or an octadecylamine or hexylamino-carbonyl-oxycholesterol moiety (Crooke et al., J. Pharmacol. Exp. Ther., 1996, 277:923). Representative United States patents that teach the preparation of such oligonucleotide conjugates have been listed above. Typical conjugation protocols involve the synthesis of oligonucleotides bearing an aminolinker at one or more positions of the sequence. The amino group is then reacted with the molecule being conjugated using appropriate coupling or activating reagents. The conjugation reaction may be performed either with the oligonucleotide still bound to the solid support or following cleavage of the oligonucleotide in solution phase. Purification of the oligonucleotide conjugate by HPLC typically affords the pure conjugate. The use of a cholesterol conjugate is particularly preferred since such a moiety can increase targeting liver cells, a site of target expression.

Vector Encoded dsRNA

The dsRNA of the invention can also be expressed from recombinant viral vectors intracellularly in vivo. The recombinant viral vectors of the invention comprise sequences encoding the dsRNA of the invention and any suitable promoter for expressing the dsRNA sequences. Suitable promoters include, for example, the U6 or H1 RNA pol III promoter sequences and the cytomegalovirus promoter. Selection of other suitable promoters is within the skill in the art. The recombinant viral vectors of the invention can also comprise inducible or regulatable promoters for expression of the dsRNA in a particular tissue or in a particular intracellular environment. The use of recombinant viral vectors to deliver dsRNA of the invention to cells in vivo is discussed in more detail below.

dsRNA of the invention can be expressed from a recombinant viral vector either as two separate, complementary RNA molecules, or as a single RNA molecule with two complementary regions.

Any viral vector capable of accepting the coding sequences for the dsRNA molecule(s) to be expressed can be used, for example vectors derived from adenovirus (AV); adeno-associated virus (AAV); retroviruses (e.g, lentiviruses (LV), Rhabdoviruses, murine leukemia virus); herpes virus, and the like. The tropism of viral vectors can be modified by pseudotyping the vectors with envelope proteins or other surface antigens from other viruses, or by substituting different viral capsid proteins, as appropriate.

For example, lentiviral vectors of the invention can be pseudotyped with surface proteins from vesicular stomatitis virus (VSV), rabies, Ebola, Mokola, and the like. AAV vectors of the invention can be made to target different cells by engineering the vectors to express different capsid protein serotypes. For example, an AAV vector expressing a serotype 2 capsid on a serotype 2 genome is called AAV 2/2. This serotype 2 capsid gene in the AAV 2/2 vector can be replaced by a serotype 5 capsid gene to produce an AAV 2/5 vector. Techniques for constructing AAV vectors which express different capsid protein serotypes are within the skill in the art; see, e.g., Rabinowitz J E et al. (2002), J Virol 76:791-801, the entire disclosure of which is herein incorporated by reference.

Selection of recombinant viral vectors suitable for use in the invention, methods for inserting nucleic acid sequences for expressing the dsRNA into the vector, and methods of delivering the viral vector to the cells of interest are within the skill in the art. See, for example, Dornburg R (1995), Gene Therap. 2: 301-310; Eglitis M A (1988), Biotechniques 6: 608-614; Miller A D (1990), Hum Gene Therap. 1: 5-14; Anderson W F (1998), Nature 392: 25-30; and Rubinson D A et al., Nat. Genet. 33: 401-406, the entire disclosures of which are herein incorporated by reference.

Preferred viral vectors are those derived from AV and AAV. In a particularly preferred embodiment, the dsRNA of the invention is expressed as two separate, complementary single-stranded RNA molecules from a recombinant AAV vector comprising, for example, either the U6 or H1 RNA promoters, or the cytomegalovirus (CMV) promoter.

A suitable AV vector for expressing the dsRNA of the invention, a method for constructing the recombinant AV vector, and a method for delivering the vector into target cells, are described in Xia H et al. (2002), Nat. Biotech. 20: 1006-1010.

Suitable AAV vectors for expressing the dsRNA of the invention, methods for constructing the recombinant AV vector, and methods for delivering the vectors into target cells are described in Samulski R et al. (1987), J. Virol. 61: 3096-3101; Fisher K J et al. (1996), J. Virol, 70: 520-532; Samulski R et al. (1989), J. Virol. 63: 3822-3826; U.S. Pat. No. 5,252,479; U.S. Pat. No. 5,139,941; International Patent Application No. WO 94/13788; and International Patent Application No. WO 93/24641, the entire disclosures of which are herein incorporated by reference.

III. PHARMACEUTICAL COMPOSITIONS

In one embodiment, the invention provides pharmaceutical compositions containing a dsRNA, as described herein, and a pharmaceutically acceptable carrier and methods of administering the same. The pharmaceutical composition containing the dsRNA is useful for treating a disease or disorder associated with the expression or activity of a target gene, such as pathological processes mediated by target gene expression. Such pharmaceutical compositions are formulated based on the mode of delivery. In an embodiment, the invention provides pharmaceutical compositions having an agent, as described herein, and a pharmaceutically acceptable carrier and methods of administering the same. In an embodiment, the invention provides pharmaceutical compositions having a dsRNA and an agent, as described herein, and a pharmaceutically acceptable carrier and methods of administering the same.

Dosage

The pharmaceutical compositions featured herein are administered in dosages sufficient to inhibit expression of target genes. In general, a suitable dose of dsRNA will be in the range of 0.01 to 200.0 milligrams per kilogram body weight of the recipient per day, generally in the range of 1 to 50 mg per kilogram body weight per day. For example, the dsRNA can be administered at 0.01 mg/kg, 0.05 mg/kg, 0.5 mg/kg, 1 mg/kg, 1.5 mg/kg, 2.0 mg/kg, 3.0 mg/kg, 5.0 mg/kg, 10 mg/kg, 20 mg/kg, 30 mg/kg, 40 mg/kg, or 50 mg/kg per single dose.

In another embodiment, the dosage is between 0.01 and 0.2 mg/kg. For example, the dsRNA can be administered at a dose of 0.01 mg/kg, 0.02 mg/kg, 0.03 mg/kg, 0.04 mg/kg, 0.05 mg/kg, 0.06 mg/kg, 0.07 mg/kg 0.08 mg/kg 0.09 mg/kg, 0.10 mg/kg, 0.11 mg/kg, 0.12 mg/kg, 0.13 mg/kg, 0.14 mg/kg, 0.15 mg/kg, 0.16 mg/kg, 0.17 mg/kg, 0.18 mg/kg, 0.19 mg/kg, or 0.20 mg/kg.

In one embodiment, the dosage is between 0.2 mg/kg and 1.5 mg/kg. For example, the dsRNA can be administered at a dose of 0.2 mg/kg, 0.3 mg/kg, 0.4 mg/kg, 0.5 mg/kg, 0.6 mg/kg, 0.7 mg/kg, 0.8 mg/kg, 0.9 mg/kg, 1 mg/kg, 1.1 mg/kg, 1.2 mg/kg, 1.3 mg/kg, 1.4 mg/kg, or 1.5 mg/kg.

The dsRNA can be administered at a dose of 0.03, 0.1, 0.3, or 1.3, or 3.0 mg/kg.

The pharmaceutical composition can be administered once daily, or the dsRNA may be administered as two, three, or more sub-doses at appropriate intervals throughout the day. The effect of a single dose on target mRNA levels is long lasting, such that subsequent doses are administered at not more than 7 day intervals, or at not more than 1, 2, 3, or 4 week intervals.

In one embodiment the lipid formulated mRNA targeted dsRNA is administered at a first dose of about 3 mg/kg followed by administering at least one subsequent dose once a week, wherein the subsequent dose is lower than the first dose, e.g., the subsequent dose is about 1.0 mg/kg or about 0.3 mg/kg. The subsequent dose can be administered, e.g., once a week for four weeks. In some embodiments the dsRNA is administered using continuous infusion or delivery through a controlled release formulation. In that case, the dsRNA contained in each sub-dose must be correspondingly smaller in order to achieve the total daily dosage. The dosage unit can also be compounded for delivery over several days, e.g., using a conventional sustained release formulation which provides sustained release of the dsRNA over a several day period. Sustained release formulations are well known in the art and are particularly useful for delivery of agents at a particular site, such as could be used with the agents of the present invention. In this embodiment, the dosage unit contains a corresponding multiple of the daily dose.

The skilled artisan will appreciate that certain factors may influence the dosage and timing required to effectively treat a subject, including but not limited to the severity of the disease or disorder, previous treatments, the general health and/or age of the subject, and other diseases present. Moreover, treatment of a subject with a therapeutically effective amount of a composition can include a single treatment or a series of treatments. Estimates of effective dosages and in vivo half-lives for the individual dsRNAs encompassed by the invention can be made using conventional methodologies or on the basis of in vivo testing using an appropriate animal model, as described elsewhere herein.

Advances in mouse genetics have generated a number of mouse models for the study of various human diseases, such as pathological processes mediated by target gene expression. Such models are used for in vivo testing of dsRNA, as well as for determining a therapeutically effective dose. A suitable mouse model is, for example, a mouse containing a plasmid expressing a human target gene. Another suitable mouse model is a transgenic mouse carrying a transgene that expresses a human target gene.

Toxicity and therapeutic efficacy of such compounds can be determined by standard pharmaceutical procedures in cell cultures or experimental animals, e.g., for determining the LD50 (the dose lethal to 50% of the population) and the ED50 (the dose therapeutically effective in 50% of the population). The dose ratio between toxic and therapeutic effects is the therapeutic index and it can be expressed as the ratio LD50/ED50. Compounds that exhibit high therapeutic indices are preferred.

The data obtained from cell culture assays and animal studies can be used in formulating a range of dosage for use in humans. The dosage of compositions featured in the invention lies generally within a range of circulating concentrations that include the ED50 with little or no toxicity. The dosage may vary within this range depending upon the dosage form employed and the route of administration utilized. For any compound used in the methods featured in the invention, the therapeutically effective dose can be estimated initially from cell culture assays. A dose may be formulated in animal models to achieve a circulating plasma concentration range of the compound or, when appropriate, of the polypeptide product of a target sequence (e.g., achieving a decreased concentration of the polypeptide) that includes the IC50 (i.e., the concentration of the test compound which achieves a half-maximal inhibition of symptoms) as determined in cell culture. Such information can be used to more accurately to determine useful doses in humans. Levels in plasma may be measured, for example, by high performance liquid chromatography.

In addition to their administration, as discussed above, the dsRNAs featured in the invention can be administered in combination with other known agents effective in treatment of pathological processes mediated by target gene expression. In any event, the administering physician can adjust the amount and timing of dsRNA administration on the basis of results observed using standard measures of efficacy known in the art or described herein.

Administration

The pharmaceutical compositions of the present invention may be administered in a number of ways depending upon whether local or systemic treatment is desired and upon the area to be treated. Administration may be topical, pulmonary, e.g., by inhalation or insufflation of powders or aerosols, including by nebulizer; intratracheal, intranasal, epidermal and transdermal, and subdermal, oral or parenteral, e.g., subcutaneous.

For example, when treating a mammal with hyperlipidemia, the dsRNA molecules are administered systemically via parental means. Parenteral administration includes intravenous, intra-arterial, subcutaneous, intraperitoneal or intramuscular injection or infusion; or intracranial, e.g., intraparenchymal, intrathecal or intraventricular, administration. For example, dsRNAs, conjugated or unconjugated or formulated with or without liposomes, can be administered intravenously to a patient. For such, a dsRNA molecule can be formulated into compositions such as sterile and non-sterile aqueous solutions, non-aqueous solutions in common solvents such as alcohols, or solutions in liquid or solid oil bases. Such solutions also can contain buffers, diluents, and other suitable additives. For parenteral, intrathecal, or intraventricular administration, a dsRNA molecule can be formulated into compositions such as sterile aqueous solutions, which also can contain buffers, diluents, and other suitable additives (e.g., penetration enhancers, carrier compounds, and other pharmaceutically acceptable carriers). Formulations are described in more detail herein.

The dsRNA can be delivered in a manner to target a particular tissue, such as the liver (e.g., the hepatocytes of the liver).

Formulations

The pharmaceutical formulations of the present invention, which may conveniently be presented in unit dosage form, may be prepared according to conventional techniques well known in the pharmaceutical industry. Such techniques include the step of bringing into association the active ingredients with the pharmaceutical carrier(s) or excipient(s). In general, the formulations are prepared by uniformly and intimately bringing into association the active ingredients with liquid carriers or finely divided solid carriers or both, and then, if necessary, shaping the product.

The compositions of the present invention may be formulated into any of many possible dosage forms such as, but not limited to, tablets, capsules, gel capsules, liquid syrups, soft gels, suppositories, and enemas. The compositions of the present invention may also be formulated as suspensions in aqueous, non-aqueous or mixed media. Aqueous suspensions may further contain substances which increase the viscosity of the suspension including, for example, sodium carboxymethylcellulose, sorbitol and/or dextran. The suspension may also contain stabilizers.

Pharmaceutical compositions of the present invention include, but are not limited to, solutions, emulsions, and liposome-containing formulations. These compositions may be generated from a variety of components that include, but are not limited to, preformed liquids, self-emulsifying solids and self-emulsifying semisolids. In one aspect are formulations that target the liver when treating hepatic disorders such as hyperlipidemia.

In addition, dsRNA that target the target gene can be formulated into compositions containing the dsRNA admixed, encapsulated, conjugated, or otherwise associated with other molecules, molecular structures, or mixtures of nucleic acids. For example, a composition containing one or more dsRNA agents that target the target gene can contain other therapeutic agents, such as other cancer therapeutics or one or more dsRNA compounds that target other target genes.

Oral, Parenteral, Topical, and Biologic Formulations

Compositions and formulations for oral administration include powders or granules, microparticulates, nanoparticulates, suspensions or solutions in water or non-aqueous media, capsules, gel capsules, sachets, tablets or minitablets. Thickeners, flavoring agents, diluents, emulsifiers, dispersing aids or binders may be desirable. In some embodiments, oral formulations are those in which dsRNAs featured in the invention are administered in conjunction with one or more penetration enhancers surfactants and chelators. Suitable surfactants include fatty acids and/or esters or salts thereof, bile acids and/or salts thereof. Suitable bile acids/salts include chenodeoxycholic acid (CDCA) and ursodeoxychenodeoxycholic acid (UDCA), cholic acid, dehydrocholic acid, deoxycholic acid, glucholic acid, glycholic acid, glycodeoxycholic acid, taurocholic acid, taurodeoxycholic acid, sodium tauro-24,25-dihydro-fusidate and sodium glycodihydrofusidate. Suitable fatty acids include arachidonic acid, undecanoic acid, oleic acid, lauric acid, caprylic acid, capric acid, myristic acid, palmitic acid, stearic acid, linoleic acid, linolenic acid, dicaprate, tricaprate, monoolein, dilaurin, glyceryl 1-monocaprate, 1-dodecylazacycloheptan-2-one, an acylcarnitine, an acylcholine, or a monoglyceride, a diglyceride or a pharmaceutically acceptable salt thereof (e.g., sodium). In some embodiments, combinations of penetration enhancers are used, for example, fatty acids/salts in combination with bile acids/salts. One exemplary combination is the sodium salt of lauric acid, capric acid and UDCA. Further penetration enhancers include polyoxyethylene-9-lauryl ether, polyoxyethylene-20-cetyl ether. dsRNAs featured in the invention may be delivered orally, in granular form including sprayed dried particles, or complexed to form micro or nanoparticles. dsRNA complexing agents include poly-amino acids; polyimines; polyacrylates; polyalkylacrylates, polyoxethanes, polyalkylcyanoacrylates; cationized gelatins, albumins, starches, acrylates, polyethyleneglycols (PEG) and starches; polyalkylcyanoacrylates; DEAE-derivatized polyimines, pollulans, celluloses and starches. Suitable complexing agents include chitosan, N-trimethylchitosan, poly-L-lysine, polyhistidine, polyornithine, polyspermines, protamine, polyvinylpyridine, polythiodiethylaminomethylethylene P(TDAE), polyaminostyrene (e.g., p-amino), poly(methylcyanoacrylate), poly(ethylcyanoacrylate), poly(butylcyanoacrylate), poly(isobutylcyanoacrylate), poly(isohexylcynaoacrylate), DEAE-methacrylate, DEAE-hexylacrylate, DEAE-acrylamide, DEAE-albumin and DEAE-dextran, polymethylacrylate, polyhexylacrylate, poly(D,L-lactic acid), poly(DL-lactic-co-glycolic acid (PLGA), alginate, and polyethyleneglycol (PEG). Oral formulations for dsRNAs and their preparation are described in detail in U.S. Pat. No. 6,887,906, U.S. Patent Publication. No. 20030027780, and U.S. Pat. No. 6,747,014, each of which is incorporated herein by reference.

Compositions and formulations for parenteral, intraparenchymal (into the brain), intrathecal, intraventricular or intrahepatic administration may include sterile aqueous solutions which may also contain buffers, diluents and other suitable additives such as, but not limited to, penetration enhancers, carrier compounds and other pharmaceutically acceptable carriers or excipients.

Pharmaceutical compositions and formulations for topical administration may include transdermal patches, ointments, lotions, creams, gels, drops, suppositories, sprays, liquids and powders. Conventional pharmaceutical carriers, aqueous, powder or oily bases, thickeners and the like may be necessary or desirable. Suitable topical formulations include those in which the dsRNAs featured in the invention are in admixture with a topical delivery agent such as lipids, liposomes, fatty acids, fatty acid esters, steroids, chelating agents and surfactants. Suitable lipids and liposomes include neutral (e.g., dioleoylphosphatidyl DOPE ethanolamine, dimyristoylphosphatidyl choline DMPC, distearolyphosphatidyl choline) negative (e.g., dimyristoylphosphatidyl glycerol DMPG) and cationic (e.g., dioleoyltetramethylaminopropyl DOTAP and dioleoylphosphatidyl ethanolamine DOTMA). dsRNAs featured in the invention may be encapsulated within liposomes or may form complexes thereto. Alternatively, dsRNAs may be complexed to lipids. Suitable fatty acids and esters include but are not limited to arachidonic acid, oleic acid, eicosanoic acid, lauric acid, caprylic acid, capric acid, myristic acid, palmitic acid, stearic acid, linoleic acid, linolenic acid, dicaprate, tricaprate, monoolein, dilaurin, glyceryl 1-monocaprate, 1-dodecylazacycloheptan-2-one, an acylcarnitine, an acylcholine, or a C₁₋₁₀ alkyl ester (e.g., isopropylmyristate IPM), monoglyceride, diglyceride or pharmaceutically acceptable salt thereof. Topical formulations are described in detail in U.S. Pat. No. 6,747,014, which is incorporated herein by reference. In addition, dsRNA molecules can be administered to a mammal as biologic or abiologic means as described in, for example, U.S. Pat. No. 6,271,359. Abiologic delivery can be accomplished by a variety of methods including, without limitation, (1) loading liposomes with a dsRNA acid molecule provided herein and (2) complexing a dsRNA molecule with lipids or liposomes to form nucleic acid-lipid or nucleic acid-liposome complexes. The liposome can be composed of cationic and neutral lipids commonly used to transfect cells in vitro. Cationic lipids can complex (e.g., charge-associate) with negatively charged nucleic acids to form liposomes. Examples of cationic liposomes include, without limitation, lipofectin, lipofectamine, lipofectace, and DOTAP. Procedures for forming liposomes are well known in the art. Liposome compositions can be formed, for example, from phosphatidylcholine, dimyristoyl phosphatidylcholine, dipalmitoyl phosphatidylcholine, dimyristoyl phosphatidylglycerol, or dioleoyl phosphatidylethanolamine. Numerous lipophilic agents are commercially available, including Lipofectin™ (Invitrogen/Life Technologies, Carlsbad, Calif.) and Effectene™ (Qiagen, Valencia, Calif.). In addition, systemic delivery methods can be optimized using commercially available cationic lipids such as DDAB or DOTAP, each of which can be mixed with a neutral lipid such as DOPE or cholesterol. In some cases, liposomes such as those described by Templeton et al. (Nature Biotechnology, 15: 647-652 (1997)) can be used. In other embodiments, polycations such as polyethyleneimine can be used to achieve delivery in vivo and ex vivo (Boletta et al., J. Am Soc. Nephrol. 7: 1728 (1996)). Additional information regarding the use of liposomes to deliver nucleic acids can be found in U.S. Pat. No. 6,271,359, PCT Publication WO 96/40964 and Morrissey, D. et al. 2005. Nat Biotechnol. 23(8):1002-7.

Biologic delivery can be accomplished by a variety of methods including, without limitation, the use of viral vectors. For example, viral vectors (e.g., adenovirus and herpes virus vectors) can be used to deliver dsRNA molecules to liver cells. Standard molecular biology techniques can be used to introduce one or more of the dsRNAs provided herein into one of the many different viral vectors previously developed to deliver nucleic acid to cells. These resulting viral vectors can be used to deliver the one or more dsRNAs to cells by, for example, infection.

Liposomal Formulations

There are many organized surfactant structures besides microemulsions that have been studied and used for the formulation of drugs. These include monolayers, micelles, bilayers and vesicles. Vesicles, such as liposomes, have attracted great interest because of their specificity and the duration of action they offer from the standpoint of drug delivery. As used in the present invention, the term “liposome” means a vesicle composed of amphiphilic lipids arranged in a spherical bilayer or bilayers.

Liposomes are unilamellar or multilamellar vesicles which have a membrane formed from a lipophilic material and an aqueous interior. The aqueous portion contains the composition to be delivered. Cationic liposomes possess the advantage of being able to fuse to the cell wall. Non-cationic liposomes, although not able to fuse as efficiently with the cell wall, are taken up by macrophages in vivo.

In order to cross intact mammalian skin, lipid vesicles must pass through a series of fine pores, each with a diameter less than 50 nm, under the influence of a suitable transdermal gradient. Therefore, it is desirable to use a liposome which is highly deformable and able to pass through such fine pores.

Further advantages of liposomes include: liposomes obtained from natural phospholipids are biocompatible and biodegradable; liposomes can incorporate a wide range of water and lipid soluble drugs; and liposomes can protect encapsulated drugs in their internal compartments from metabolism and degradation (Rosoff, in Pharmaceutical Dosage Forms, Lieberman, Rieger and Banker (Eds.), 1988, Marcel Dekker, Inc., New York, N.Y., volume 1, p. 245). Important considerations in the preparation of liposome formulations are the lipid surface charge, vesicle size and the aqueous volume of the liposomes.

Liposomes are useful for the transfer and delivery of active ingredients to the site of action. Because the liposomal membrane is structurally similar to biological membranes, when liposomes are applied to a tissue, the liposomes start to merge with the cellular membranes and as the merging of the liposome and cell progresses, the liposomal contents are emptied into the cell where the active agent may act.

Liposomal formulations have been the focus of extensive investigation as the mode of delivery for many drugs. There is growing evidence that for topical administration, liposomes present several advantages over other formulations. Such advantages include reduced side-effects related to high systemic absorption of the administered drug, increased accumulation of the administered drug at the desired target, and the ability to administer a wide variety of drugs, both hydrophilic and hydrophobic, into the skin.

Several reports have detailed the ability of liposomes to deliver agents including high-molecular weight DNA into the skin. Compounds including analgesics, antibodies, hormones and high-molecular weight DNAs have been administered to the skin. The majority of applications resulted in the targeting of the upper epidermis

Liposomes fall into two broad classes. Cationic liposomes are positively charged liposomes which interact with the negatively charged DNA molecules to form a stable complex. The positively charged DNA/liposome complex binds to the negatively charged cell surface and is internalized in an endosome. Due to the acidic pH within the endosome, the liposomes are ruptured, releasing their contents into the cell cytoplasm (Wang et al., Biochem. Biophys. Res. Commun., 1987, 147, 980-985).

Liposomes which are pH-sensitive or negatively-charged, entrap DNA rather than complex with it. Since both the DNA and the lipid are similarly charged, repulsion rather than complex formation occurs. Nevertheless, some DNA is entrapped within the aqueous interior of these liposomes. pH-sensitive liposomes have been used to deliver DNA encoding the thymidine kinase gene to cell monolayers in culture. Expression of the exogenous gene was detected in the target cells (Zhou et al., Journal of Controlled Release, 1992, 19, 269-274).

One major type of liposomal composition includes phospholipids other than naturally-derived phosphatidylcholine. Neutral liposome compositions, for example, can be formed from dimyristoyl phosphatidylcholine (DMPC) or dipalmitoyl phosphatidylcholine (DPPC). Anionic liposome compositions generally are formed from dimyristoyl phosphatidylglycerol, while anionic fusogenic liposomes are formed primarily from dioleoyl phosphatidylethanolamine (DOPE). Another type of liposomal composition is formed from phosphatidylcholine (PC) such as, for example, soybean PC, and egg PC. Another type is formed from mixtures of phospholipid and/or phosphatidylcholine and/or cholesterol.

Several studies have assessed the topical delivery of liposomal drug formulations to the skin. Application of liposomes containing interferon to guinea pig skin resulted in a reduction of skin herpes sores while delivery of interferon via other means (e.g., as a solution or as an emulsion) were ineffective (Weiner et al., Journal of Drug Targeting, 1992, 2, 405-410). Further, an additional study tested the efficacy of interferon administered as part of a liposomal formulation to the administration of interferon using an aqueous system, and concluded that the liposomal formulation was superior to aqueous administration (du Plessis et al., Antiviral Research, 1992, 18, 259-265).

Non-ionic liposomal systems have also been examined to determine their utility in the delivery of drugs to the skin, in particular systems comprising non-ionic surfactant and cholesterol. Non-ionic liposomal formulations comprising Novasome™ I (glyceryl dilaurate/cholesterol/polyoxyethylene-10-stearyl ether) and Novasome™ II (glyceryl distearate/cholesterol/polyoxyethylene-10-stearyl ether) were used to deliver cyclosporin-A into the dermis of mouse skin. Results indicated that such non-ionic liposomal systems were effective in facilitating the deposition of cyclosporin-A into different layers of the skin (Hu et al., S.T.P. Pharma. Sci., 1994, 4, 6, 466).

Liposomes also include “sterically stabilized” liposomes, a term which, as used herein, refers to liposomes comprising one or more specialized lipids that, when incorporated into liposomes, result in enhanced circulation lifetimes relative to liposomes lacking such specialized lipids. Examples of sterically stabilized liposomes are those in which part of the vesicle-forming lipid portion of the liposome (A) comprises one or more glycolipids, such as monosialoganglioside G_(M1), or (B) is derivatized with one or more hydrophilic polymers, such as a polyethylene glycol (PEG) moiety. While not wishing to be bound by any particular theory, it is thought in the art that, at least for sterically stabilized liposomes containing gangliosides, sphingomyelin, or PEG-derivatized lipids, the enhanced circulation half-life of these sterically stabilized liposomes derives from a reduced uptake into cells of the reticuloendothelial system (RES) (Allen et al., FEBS Letters, 1987, 223, 42; Wu et al., Cancer Research, 1993, 53, 3765).

Various liposomes comprising one or more glycolipids are known in the art. Papahadjopoulos et al. (Ann. N.Y. Acad. Sci., 1987, 507, 64) reported the ability of monosialoganglioside G_(M1), galactocerebroside sulfate and phosphatidylinositol to improve blood half-lives of liposomes. These findings were expounded upon by Gabizon et al. (Proc. Natl. Acad. Sci. U.S.A., 1988, 85, 6949). U.S. Pat. No. 4,837,028 and WO 88/04924, both to Allen et al., disclose liposomes comprising (1) sphingomyelin and (2) the ganglioside G_(M1) or a galactocerebroside sulfate ester. U.S. Pat. No. 5,543,152 (Webb et al.) discloses liposomes comprising sphingomyelin. Liposomes comprising 1,2-sn-dimyristoylphosphatidylcholine are disclosed in WO 97/13499 (Lim et al.).

Many liposomes comprising lipids derivatized with one or more hydrophilic polymers, and methods of preparation thereof, are known in the art. Sunamoto et al. (Bull. Chem. Soc. Jpn., 1980, 53, 2778) described liposomes comprising a nonionic detergent, 2C_(1215G), that contains a PEG moiety. Illum et al. (FEBS Lett., 1984, 167, 79) noted that hydrophilic coating of polystyrene particles with polymeric glycols results in significantly enhanced blood half-lives. Synthetic phospholipids modified by the attachment of carboxylic groups of polyalkylene glycols (e.g., PEG) are described by Sears (U.S. Pat. Nos. 4,426,330 and 4,534,899). Klibanov et al. (FEBS Lett., 1990, 268, 235) described experiments demonstrating that liposomes comprising phosphatidylethanolamine (PE) derivatized with PEG or PEG stearate have significant increases in blood circulation half-lives. Blume et al. (Biochimica et Biophysica Acta, 1990, 1029, 91) extended such observations to other PEG-derivatized phospholipids, e.g., DSPE-PEG, formed from the combination of distearoylphosphatidylethanolamine (DSPE) and PEG. Liposomes having covalently bound PEG moieties on their external surface are described in European Patent No. EP 0 445 131 B1 and WO 90/04384 to Fisher. Liposome compositions containing 1-20 mole percent of PE derivatized with PEG, and methods of use thereof, are described by Woodle et al. (U.S. Pat. Nos. 5,013,556 and 5,356,633) and Martin et al. (U.S. Pat. No. 5,213,804 and European Patent No. EP 0 496 813 B1). Liposomes comprising a number of other lipid-polymer conjugates are disclosed in WO 91/05545 and U.S. Pat. No. 5,225,212 (both to Martin et al.) and in WO 94/20073 (Zalipsky et al.) Liposomes comprising PEG-modified ceramide lipids are described in WO 96/10391 (Choi et al). U.S. Pat. No. 5,540,935 (Miyazaki et al.) and U.S. Pat. No. 5,556,948 (Tagawa et al.) describe PEG-containing liposomes that can be further derivatized with functional moieties on their surfaces.

A number of liposomes comprising nucleic acids are known in the art. WO 96/40062 to Thierry et al. discloses methods for encapsulating high molecular weight nucleic acids in liposomes. U.S. Pat. No. 5,264,221 to Tagawa et al. discloses protein-bonded liposomes and asserts that the contents of such liposomes may include a dsRNA. U.S. Pat. No. 5,665,710 to Rahman et al. describes certain methods of encapsulating oligodeoxynucleotides in liposomes. WO 97/04787 to Love et al. discloses liposomes comprising dsRNAs targeted to the raf gene.

Transfersomes are yet another type of liposomes and are highly deformable lipid aggregates which are attractive candidates for drug delivery vehicles. Transfersomes may be described as lipid droplets which are so highly deformable that they are easily able to penetrate through pores which are smaller than the droplet. Transfersomes are adaptable to the environment in which they are used, e.g., they are self-optimizing (adaptive to the shape of pores in the skin), self-repairing, frequently reach their targets without fragmenting, and often self-loading. To make transfersomes, it is possible to add surface edge-activators, usually surfactants, to a standard liposomal composition. Transfersomes have been used to deliver serum albumin to the skin. The transfersome-mediated delivery of serum albumin has been shown to be as effective as subcutaneous injection of a solution containing serum albumin.

Surfactants find wide application in formulations such as emulsions (including microemulsions) and liposomes. The most common way of classifying and ranking the properties of the many different types of surfactants, both natural and synthetic, is by the use of the hydrophile/lipophile balance (HLB). The nature of the hydrophilic group (also known as the “head”) provides the most useful means for categorizing the different surfactants used in formulations (Rieger, in Pharmaceutical Dosage Forms, Marcel Dekker, Inc., New York, N.Y., 1988, p. 285).

If the surfactant molecule is not ionized, it is classified as a nonionic surfactant. Nonionic surfactants find wide application in pharmaceutical and cosmetic products and are usable over a wide range of pH values. In general their HLB values range from 2 to about 18 depending on their structure. Nonionic surfactants include nonionic esters such as ethylene glycol esters, propylene glycol esters, glyceryl esters, polyglyceryl esters, sorbitan esters, sucrose esters, and ethoxylated esters. Nonionic alkanolamides and ethers such as fatty alcohol ethoxylates, propoxylated alcohols, and ethoxylated/propoxylated block polymers are also included in this class. The polyoxyethylene surfactants are the most popular members of the nonionic surfactant class.

If the surfactant molecule carries a negative charge when it is dissolved or dispersed in water, the surfactant is classified as anionic. Anionic surfactants include carboxylates such as soaps, acyl lactylates, acyl amides of amino acids, esters of sulfuric acid such as alkyl sulfates and ethoxylated alkyl sulfates, sulfonates such as alkyl benzene sulfonates, acyl isethionates, acyl taurates and sulfosuccinates, and phosphates. The most important members of the anionic surfactant class are the alkyl sulfates and the soaps.

If the surfactant molecule carries a positive charge when it is dissolved or dispersed in water, the surfactant is classified as cationic. Cationic surfactants include quaternary ammonium salts and ethoxylated amines. The quaternary ammonium salts are the most used members of this class.

If the surfactant molecule has the ability to carry either a positive or negative charge, the surfactant is classified as amphoteric. Amphoteric surfactants include acrylic acid derivatives, substituted alkylamides, N-alkylbetaines and phosphatides.

The use of surfactants in drug products, formulations and in emulsions has been reviewed (Rieger, in Pharmaceutical Dosage Forms, Marcel Dekker, Inc., New York, N.Y., 1988, p. 285).

Nucleic Acid Lipid Particles

In one embodiment, a dsRNA featured in the invention (e.g., a dsRNA targeting a gene of interest or, e.g., an agent such as a dsRNA targeting an Ebola gene) is fully encapsulated in the lipid formulation, e.g., to form a nucleic acid-lipid particle. Nucleic acid-lipid particles typically contain a cationic lipid, a non-cationic lipid, a sterol, and a lipid that prevents aggregation of the particle (e.g., a PEG-lipid conjugate). Nucleic acid-lipid particles are extremely useful for systemic applications, as they exhibit extended circulation lifetimes following intravenous (i.v.) injection and accumulate at distal sites (e.g., sites physically separated from the administration site). In addition, the nucleic acids when present in the nucleic acid-lipid particles of the present invention are resistant in aqueous solution to degradation with a nuclease. Nucleic acid-lipid particles and their method of preparation are disclosed in, e.g., U.S. Pat. Nos. 5,976,567; 5,981,501; 6,534,484; 6,586,410; 6,815,432; and PCT Publication No. WO 96/40964.

Nucleic acid-lipid particles can further include one or more additional lipids and/or other components such as cholesterol. Other lipids may be included in the liposome compositions for a variety of purposes, such as to prevent lipid oxidation or to attach ligands onto the liposome surface. Any of a number of lipids may be present, including amphipathic, neutral, cationic, and anionic lipids. Such lipids can be used alone or in combination. Specific examples of additional lipid components that may be present are described herein.

Additional components that may be present in a nucleic acid-lipid particle include bilayer stabilizing components such as polyamide oligomers (see, e.g., U.S. Pat. No. 6,320,017), peptides, proteins, detergents, lipid-derivatives, such as PEG coupled to phosphatidylethanolamine and PEG conjugated to ceramides (see, U.S. Pat. No. 5,885,613).

A nucleic acid-lipid particle can include one or more of a second amino lipid or cationic lipid, a neutral lipid, a sterol, and a lipid selected to reduce aggregation of lipid particles during formation, which may result from steric stabilization of particles which prevents charge-induced aggregation during formation.

Nucleic acid-lipid particles include, e.g., a SPLP, pSPLP, and SNALP. The term“SNALP” refers to a stable nucleic acid-lipid particle, including SPLP. The term “SPLP” refers to a nucleic acid-lipid particle comprising plasmid DNA encapsulated within a lipid vesicle. SPLPs include “pSPLP,” which include an encapsulated condensing agent-nucleic acid complex as set forth in PCT Publication No. WO 00/03683.

The particles of the present invention typically have a mean diameter of about 50 nm to about 150 nm, more typically about 60 nm to about 130 nm, more typically about 70 nm to about 110 nm, most typically about 70 nm to about 90 nm, and are substantially nontoxic

In one embodiment, the lipid to drug ratio (mass/mass ratio) (e.g., lipid to dsRNA ratio) will be in the range of from about 1:1 to about 50:1, from about 1:1 to about 25:1, from about 3:1 to about 15:1, from about 4:1 to about 10:1, from about 5:1 to about 9:1, or about 6:1 to about 9:1, or about 6:1, 7:1, 8:1, 9:1, 10:1, 11:1, 12:1, or 33:1.

Cationic Lipids

Cationic lipids can include ionizable cationic lipids and non-ionizable cationic lipids. A cationic lipid may be, for example, N,N-dioleyl-N,N-dimethylammonium chloride (DODAC), N,N-distearyl-N,N-dimethylammonium bromide (DDAB), N—(I-(2,3-dioleoyloxy)propyl)-N,N,N-trimethylammonium chloride (DOTAP), N—(I-(2,3-dioleyloxy)propyl)-N,N,N-trimethylammonium chloride (DOTMA), N,N-dimethyl-2,3-dioleyloxy)propylamine (DODMA), 1,2-DiLinoleyloxy-N,N-dimethylaminopropane (DLinDMA), 1,2-Dilinolenyloxy-N,N-dimethylaminopropane (DLenDMA), 1,2-Dilinoleylcarbamoyloxy-3-dimethylaminopropane (DLin-C-DAP), 1,2-Dilinoleyoxy-3-(dimethylamino)acetoxypropane (DLin-DAC), 1,2-Dilinoleyoxy-3-morpholinopropane (DLin-MA), 1,2-Dilinoleoyl-3-dimethylaminopropane (DLinDAP), 1,2-Dilinoleylthio-3-dimethylaminopropane (DLin-S-DMA), 1-Linoleoyl-2-linoleyloxy-3-dimethylaminopropane (DLin-2-DMAP), 1,2-Dilinoleyloxy-3-trimethylaminopropane chloride salt (DLin-TMA.Cl), 1,2-Dilinoleoyl-3-trimethylaminopropane chloride salt (DLin-TAP.Cl), 1,2-Dilinoleyloxy-3-(N-methylpiperazino)propane (DLin-MPZ), or 3-(N,N-Dilinoleylamino)-1,2-propanediol (DLinAP), 3-(N,N-Dioleylamino)-1,2-propanedio (DOAP), 1,2-Dilinoleyloxo-3-(2-N,N-dimethylamino)ethoxypropane (DLin-EG-DMA), 1,2-Dilinolenyloxy-N,N-dimethylaminopropane (DLinDMA), 2,2-Dilinoleyl-4-dimethylaminomethyl-[1,3]-dioxolane (DLin-K-DMA) or analogs thereof, (3aR,5s,6aS)-N,N-dimethyl-2,2-di((9Z,12Z)-octadeca-9,12-di enyl)tetrahydro-3aH-cyclopenta[d][1,3]dioxol-5-amine (ALNY-100), (6Z,9Z,28Z,31Z)-heptatriaconta-6,9,28,31-tetraen-19-yl 4-(dimethylamino)butanoate (MC3), or a mixture thereof.

Other cationic lipids, which carry a net positive charge at about physiological pH, in addition to those specifically described above, may also be included in lipid particles of the invention. Such cationic lipids include, but are not limited to, N,N-dioleyl-N,N-dimethylammonium chloride (“DODAC”); N-(2,3-dioleyloxyl)propyl-N,N—N-triethylammonium chloride (“DOTMA”); N,N-distearyl-N,N-dimethylammonium bromide (“DDAB”); N-(2,3-dioleoyloxy)propyl)-N,N,N-trimethylammonium chloride (“DOTAP”); 1,2-Dioleyloxy-3-trimethylaminopropane chloride salt (“DOTAP.Cl”); 3β-(N—(N′,N′-dimethylaminoethane)-carbamoyl)cholesterol (“DC-Chol”), N-(1-(2,3-dioleyloxyl)propyl)-N-2-(sperminecarboxamido)ethyl)-N,N-dimethylammonium trifluoracetate (“DOSPA”), dioctadecylamidoglycyl carboxyspermine (“DOGS”), 1,2-dileoyl-sn-3-phosphoethanolamine (“DOPE”), 1,2-dioleoyl-3-dimethylammonium propane (“DODAP”), N, N-dimethyl-2,3-dioleyloxy)propylamine (“DODMA”), and N-(1,2-dimyristyloxyprop-3-yl)-N,N-dimethyl-N-hydroxyethyl ammonium bromide (“DMRIE”). Additionally, a number of commercial preparations of cationic lipids can be used, such as, e.g., LIPOFECTIN (including DOTMA and DOPE, available from GIBCO/BRL), and LIPOFECTAMINE (comprising DOSPA and DOPE, available from GIBCO/BRL). In particular embodiments, a cationic lipid is an amino lipid.

As used herein, the term “amino lipid” is meant to include those lipids having one or two fatty acid or fatty alkyl chains and an amino head group (including an alkylamino or dialkylamino group) that may be protonated to form a cationic lipid at physiological pH.

Other amino lipids would include those having alternative fatty acid groups and other dialkylamino groups, including those in which the alkyl substituents are different (e.g., N-ethyl-N-methylamino-, N-propyl-N-ethylamino- and the like). For those embodiments in which R¹¹ and R¹² are both long chain alkyl or acyl groups, they can be the same or different. In general, amino lipids having less saturated acyl chains are more easily sized, particularly when the complexes must be sized below about 0.3 microns, for purposes of filter sterilization. Amino lipids containing unsaturated fatty acids with carbon chain lengths in the range of C₁₄ to C₂₂ are preferred. Other scaffolds can also be used to separate the amino group and the fatty acid or fatty alkyl portion of the amino lipid. Suitable scaffolds are known to those of skill in the art.

In certain embodiments, amino or cationic lipids of the invention have at least one protonatable or deprotonatable group, such that the lipid is positively charged at a pH at or below physiological pH (e.g. pH 7.4), and neutral at a second pH, preferably at or above physiological pH. It will, of course, be understood that the addition or removal of protons as a function of pH is an equilibrium process, and that the reference to a charged or a neutral lipid refers to the nature of the predominant species and does not require that all of the lipid be present in the charged or neutral form. Lipids that have more than one protonatable or deprotonatable group, or which are zwiterrionic, are not excluded from use in the invention.

In certain embodiments, protonatable lipids according to the invention have a pKa of the protonatable group in the range of about 4 to about 11. Most preferred is pKa of about 4 to about 7, because these lipids will be cationic at a lower pH formulation stage, while particles will be largely (though not completely) surface neutralized at physiological pH around pH 7.4. One of the benefits of this pKa is that at least some nucleic acid associated with the outside surface of the particle will lose its electrostatic interaction at physiological pH and be removed by simple dialysis; thus greatly reducing the particle's susceptibility to clearance.

One example of a cationic lipid is 1,2-Dilinolenyloxy-N,N-dimethylaminopropane (DLinDMA). Synthesis and preparation of nucleic acid-lipid particles including DlinDMA is described in International application number PCT/CA2009/00496, filed Apr. 15, 2009.

In one embodiment, the cationic lipid XTC (2,2-Dilinoleyl-4-dimethylaminoethyl-[1,3]-dioxolane) is used to prepare nucleic acid-lipid particles. Synthesis of XTC is described, e.g., in PCT/US10/22614 filed on Jan. 29, 2010, which is hereby incorporated by reference.

In another embodiment, the cationic lipid MC3 ((6Z,9Z,28Z,31Z)-heptatriaconta-6,9,28,31-tetraen-19-yl 4-(dimethylamino)butanoate), (e.g., DLin-M-C3-DMA) is used to prepare nucleic acid-lipid particles. Synthesis of MC3 and MC3 comprising formulations are described, e.g., in U.S. Ser. No. 12/813,448, filed Jun. 10, 2010, which is hereby incorporated by reference.

In another embodiment, the cationic lipid ALNY-100 ((3 aR,5s,6aS)-N,N-dimethyl-2,2-di((9Z,12Z)-octadeca-9,12-dienyl)tetrahydro-3aH-cyclopenta[d][1,3]dioxol-5-amine) is used to prepare nucleic acid-lipid particles. Synthesis of ALNY-100 is described in International patent application number PCT/US09/63933 filed on Nov. 10, 2009, which is herein incorporated by reference.

The cationic lipid may comprise from about 20 mol % to about 70 mol % or about 45-65 mol % or about 40 mol % of the total lipid present in the particle.

Non-Cationic Lipids

The nucleic acid-lipid particles of the invention can include a non-cationic lipid. The non-cationic lipid may be an anionic lipid or a neutral lipid. Examples include but not limited to, distearoylphosphatidylcholine (DSPC), dioleoylphosphatidylcholine (DOPC), dipalmitoylphosphatidylcholine (DPPC), dioleoylphosphatidylglycerol (DOPG), dipalmitoylphosphatidylglycerol (DPPG), dioleoyl-phosphatidylethanolamine (DOPE), palmitoyloleoylphosphatidylcholine (POPC), palmitoyloleoylphosphatidylethanolamine (POPE), dioleoyl-phosphatidylethanolamine 4-(N-maleimidomethyl)-cyclohexane-1-carboxylate (DOPE-mal), dipalmitoyl phosphatidyl ethanolamine (DPPE), dimyristoylphosphoethanolamine (DMPE), distearoyl-phosphatidyl-ethanolamine (DSPE), 16-O-monomethyl PE, 16-O-dimethyl PE, 18-1-trans PE, 1-stearoyl-2-olcoyl-phosphatidylethanolamine (SOPE), cholesterol, or a mixture thereof.

Anionic lipids suitable for use in lipid particles of the invention include, but are not limited to, phosphatidylglycerol, cardiolipin, diacylphosphatidylserine, diacylphosphatidic acid, N-dodecanoyl phosphatidylethanoloamine, N-succinyl phosphatidylethanolamine, N-glutaryl phosphatidylethanolamine, lysylphosphatidylglycerol, and other anionic modifying groups joined to neutral lipids.

Neutral lipids, when present in the lipid particle, can be any of a number of lipid species which exist either in an uncharged or neutral zwitterionic form at physiological pH. Such lipids include, for example diacylphosphatidylcholine, diacylphosphatidylethanolamine, ceramide, sphingomyelin, dihydrosphingomyelin, cephalin, and cerebrosides. The selection of neutral lipids for use in the particles described herein is generally guided by consideration of, e.g., liposome size and stability of the liposomes in the bloodstream. Preferably, the neutral lipid component is a lipid having two acyl groups, (i.e., diacylphosphatidylcholine and diacylphosphatidylethanolamine). Lipids having a variety of acyl chain groups of varying chain length and degree of saturation are available or may be isolated or synthesized by well-known techniques. In one group of embodiments, lipids containing saturated fatty acids with carbon chain lengths in the range of C₁₄ to C₂₂ are preferred. In another group of embodiments, lipids with mono- or di-unsaturated fatty acids with carbon chain lengths in the range of C₁₄ to C₂₂ are used. Additionally, lipids having mixtures of saturated and unsaturated fatty acid chains can be used. Preferably, the neutral lipids used in the invention are DOPE, DSPC, POPC, or any related phosphatidylcholine. The neutral lipids useful in the invention may also be composed of sphingomyelin, dihydrosphingomyeline, or phospholipids with other head groups, such as serine and inositol.

In one embodiment the non-cationic lipid is distearoylphosphatidylcholine (DSPC). In another embodiment the non-cationic lipid is dipalmitoylphosphatidylcholine (DPPC).

The non-cationic lipid may be from about 5 mol % to about 90 mol %, about 5 mol % to about 10 mol %, about 10 mol %, or about 58 mol % if cholesterol is included, of the total lipid present in the particle.

Conjugated Lipids

Conjugated lipids can be used in nucleic acid-lipid particle to prevent aggregation, including polyethylene glycol (PEG)-modified lipids, monosialoganglioside Gm1, and polyamide oligomers (“PAO”) such as (described in U.S. Pat. No. 6,320,017). Other compounds with uncharged, hydrophilic, steric-barrier moieties, which prevent aggregation during formulation, like PEG, Gm1 or ATTA, can also be coupled to lipids for use as in the methods and compositions of the invention. ATTA-lipids are described, e.g., in U.S. Pat. No. 6,320,017, and PEG-lipid conjugates are described, e.g., in U.S. Pat. Nos. 5,820,873, 5,534,499 and 5,885,613. Typically, the concentration of the lipid component selected to reduce aggregation is about 1 to 15% (by mole percent of lipids).

Specific examples of PEG-modified lipids (or lipid-polyoxyethylene conjugates) that are useful in the invention can have a variety of “anchoring” lipid portions to secure the PEG portion to the surface of the lipid vesicle. Examples of suitable PEG-modified lipids include PEG-modified phosphatidylethanolamine and phosphatidic acid, PEG-ceramide conjugates (e.g., PEG-CerC14 or PEG-CerC20) which are described in co-pending U.S. Ser. No. 08/486,214, incorporated herein by reference, PEG-modified dialkylamines and PEG-modified 1,2-diacyloxypropan-3-amines. Particularly preferred are PEG-modified diacylglycerols and dialkylglycerols.

In embodiments where a sterically-large moiety such as PEG or ATTA are conjugated to a lipid anchor, the selection of the lipid anchor depends on what type of association the conjugate is to have with the lipid particle. It is well known that mePEG (mw2000)-diastearoylphosphatidylethanolamine (PEG-DSPE) will remain associated with a liposome until the particle is cleared from the circulation, possibly a matter of days. Other conjugates, such as PEG-CerC20 have similar staying capacity. PEG-CerC14, however, rapidly exchanges out of the formulation upon exposure to serum, with a T_(1/2) less than 60 mins. in some assays. As illustrated in US patent application Ser. No. 08/486,214, at least three characteristics influence the rate of exchange: length of acyl chain, saturation of acyl chain, and size of the steric-barrier head group. Compounds having suitable variations of these features may be useful for the invention. For some therapeutic applications, it may be preferable for the PEG-modified lipid to be rapidly lost from the nucleic acid-lipid particle in vivo and hence the PEG-modified lipid will possess relatively short lipid anchors. In other therapeutic applications, it may be preferable for the nucleic acid-lipid particle to exhibit a longer plasma circulation lifetime and hence the PEG-modified lipid will possess relatively longer lipid anchors. Exemplary lipid anchors include those having lengths of from about C₁₄ to about C₂₂, preferably from about C₁₄ to about C₁₆. In some embodiments, a PEG moiety, for example an mPEG-NH₂, has a size of about 1000, 2000, 5000, 10,000, 15,000 or 20,000 daltons.

It should be noted that aggregation preventing compounds do not necessarily require lipid conjugation to function properly. Free PEG or free ATTA in solution may be sufficient to prevent aggregation. If the particles are stable after formulation, the PEG or ATTA can be dialyzed away before administration to a subject.

The conjugated lipid that inhibits aggregation of particles may be, for example, a polyethyleneglycol (PEG)-lipid including, without limitation, a PEG-diacylglycerol (DAG), a PEG-dialkyloxypropyl (DAA), a PEG-phospholipid, a PEG-ceramide (Cer), or a mixture thereof. The PEG-DAA conjugate may be, for example, a PEG-dilauryloxypropyl (Ci₂), a PEG-dimyristyloxypropyl (Ci₄), a PEG-dipalmityloxypropyl (Ci₆), or a PEG-distearyloxypropyl (C18). Additional conjugated lipids include polyethylene glycol-didimyristoyl glycerol (C14-PEG or PEG-C14, where PEG has an average molecular weight of 2000 Da) (PEG-DMG); (R)-2,3-bis(octadecyloxy)propyl 1-(methoxy poly(ethylene glycol)2000)propylcarbamate) (PEG-DSG); PEG-carbamoyl-1,2-dimyristyloxypropylamine, in which PEG has an average molecular weight of 2000 Da (PEG-cDMA); N-Acetylgalactosamine-((R)-2,3-bis(octadecyloxy)propyl1-(methoxy poly(ethylene glycol)2000)propylcarbamate)) (GalNAc-PEG-DSG); and polyethylene glycol-dipalmitoylglycerol (PEG-DPG).

In one embodiment the conjugated lipid is PEG-DMG. In another embodiment the conjugated lipid is PEG-cDMA. In still another embodiment the conjugated lipid is PEG-DPG. Alternatively the conjugated lipid is GalNAc-PEG-DSG.

The conjugated lipid that prevents aggregation of particles may be from 0 mol % to about 20 mol % or about 0.5 to about 5.0 mol % or about 2 mol % of the total lipid present in the particle.

The sterol component of the lipid mixture, when present, can be any of those sterols conventionally used in the field of liposome, lipid vesicle or lipid particle preparation. A preferred sterol is cholesterol.

In some embodiments, the nucleic acid-lipid particle further includes a sterol, e.g., a cholesterol at, e.g., about 10 mol % to about 60 mol % or about 25 to about 40 mol % or about 48 mol % of the total lipid present in the particle.

Lipoproteins

In one embodiment, the formulations of the invention further comprise an apolipoprotein. As used herein, the term “apolipoprotein” or “lipoprotein” refers to apolipoproteins known to those of skill in the art and variants and fragments thereof and to apolipoprotein agonists, analogues or fragments thereof described below.

Suitable apolipoproteins include, but are not limited to, ApoA-I, ApoA-II, ApoA-IV, ApoA-V and ApoE, and active polymorphic forms, isoforms, variants and mutants as well as fragments or truncated forms thereof. In certain embodiments, the apolipoprotein is a thiol containing apolipoprotein. “Thiol containing apolipoprotein” refers to an apolipoprotein, variant, fragment or isoform that contains at least one cysteine residue. The most common thiol containing apolipoproteins are ApoA-I Milano (ApoA-I_(M)) and ApoA-I Paris (ApoA-I_(P)) which contain one cysteine residue (Jia et al., 2002, Biochem. Biophys. Res. Comm. 297: 206-13; Bielicki and Oda, 2002, Biochemistry 41: 2089-96). ApoA-II, ApoE2 and ApoE3 are also thiol containing apolipoproteins. Isolated ApoE and/or active fragments and polypeptide analogues thereof, including recombinantly produced forms thereof, are described in U.S. Pat. Nos. 5,672,685; 5,525,472; 5,473,039; 5,182,364; 5,177,189; 5,168,045; 5,116,739; the disclosures of which are herein incorporated by reference. ApoE3 is disclosed in Weisgraber, et al., “Human E apoprotein heterogeneity: cysteine-arginine interchanges in the amino acid sequence of the apo-E isoforms,” J. Biol. Chem. (1981) 256: 9077-9083; and Rall, et al., “Structural basis for receptor binding heterogeneity of apolipoprotein E from type III hyperlipoproteinemic subjects,” Proc. Nat. Acad. Sci. (1982) 79: 4696-4700. (See also GenBank accession number K00396.)

In certain embodiments, the apolipoprotein can be in its mature form, in its preproapolipoprotein form or in its proapolipoprotein form. Homo- and heterodimers (where feasible) of pro- and mature ApoA-I (Duverger et al., 1996, Arterioscler. Thromb. Vasc. Biol. 16(12):1424-29), ApoA-I Milano (Kion et al., 2000, Biophys. J. 79:(3)1679-87; Franceschini et al., 1985, J. Biol. Chem. 260: 1632-35), ApoA-I Paris (Daum et al., 1999, J. Mol. Med. 77:614-22), ApoA-II (Shelness et al., 1985, J. Biol. Chem. 260(14):8637-46; Shelness et al., 1984, J. Biol. Chem. 259(15):9929-35), ApoA-IV (Duverger et al., 1991, Euro. J. Biochem. 201(2):373-83), and ApoE (McLean et al., 1983, J. Biol. Chem. 258(14):8993-9000) can also be utilized within the scope of the invention.

In certain embodiments, the apolipoprotein can be a fragment, variant or isoform of the apolipoprotein. The term “fragment” refers to any apolipoprotein having an amino acid sequence shorter than that of a native apolipoprotein and which fragment retains the activity of native apolipoprotein, including lipid binding properties. By “variant” is meant substitutions or alterations in the amino acid sequences of the apolipoprotein, which substitutions or alterations, e.g., additions and deletions of amino acid residues, do not abolish the activity of native apolipoprotein, including lipid binding properties. Thus, a variant can comprise a protein or peptide having a substantially identical amino acid sequence to a native apolipoprotein provided herein in which one or more amino acid residues have been conservatively substituted with chemically similar amino acids. Examples of conservative substitutions include the substitution of at least one hydrophobic residue such as isoleucine, valine, leucine or methionine for another. Likewise, the present invention contemplates, for example, the substitution of at least one hydrophilic residue such as, for example, between arginine and lysine, between glutamine and asparagine, and between glycine and serine (see U.S. Pat. Nos. 6,004,925, 6,037,323 and 6,046,166). The term “isoform” refers to a protein having the same, greater or partial function and similar, identical or partial sequence, and may or may not be the product of the same gene and usually tissue specific (see Weisgraber 1990, J. Lipid Res. 31(8):1503-11; Hixson and Powers 1991, J. Lipid Res. 32(9):1529-35; Lackner et al., 1985, J. Biol. Chem. 260(2):703-6; Hoeg et al., 1986, J. Biol. Chem. 261(9):3911-4; Gordon et al., 1984, J. Biol. Chem. 259(1):468-74; Powell et al., 1987, Cell 50(6):831-40; Aviram et al., 1998, Arterioscler. Thromb. Vase. Biol. 18(10):1617-24; Aviram et al., 1998, J. Clin. Invest. 101(8):1581-90; Billecke et al., 2000, Drug Metab. Dispos. 28(11):1335-42; Draganov et al., 2000, J. Biol. Chem. 275(43):33435-42; Steinmetz and Utermann 1985, J. Biol. Chem. 260(4):2258-64; Widler et al., 1980, J. Biol. Chem. 255(21):10464-71; Dyer et al., 1995, J. Lipid Res. 36(1):80-8; Sacre et al., 2003, FEBS Lett. 540(1-3):181-7; Weers, et al., 2003, Biophys. Chem. 100(1-3):481-92; Gong et al., 2002, J. Biol. Chem. 277(33):29919-26; Ohta et al., 1984, J. Biol. Chem. 259(23):14888-93 and U.S. Pat. No. 6,372,886).

In certain embodiments, the methods and compositions of the present invention include the use of a chimeric construction of an apolipoprotein. For example, a chimeric construction of an apolipoprotein can be comprised of an apolipoprotein domain with high lipid binding capacity associated with an apolipoprotein domain containing ischemia reperfusion protective properties. A chimeric construction of an apolipoprotein can be a construction that includes separate regions within an apolipoprotein (i.e., homologous construction) or a chimeric construction can be a construction that includes separate regions between different apolipoproteins (i.e., heterologous constructions). Compositions comprising a chimeric construction can also include segments that are apolipoprotein variants or segments designed to have a specific character (e.g., lipid binding, receptor binding, enzymatic, enzyme activating, antioxidant or reduction-oxidation property) (see Weisgraber 1990, J. Lipid Res. 31(8):1503-11; Hixson and Powers 1991, J. Lipid Res. 32(9):1529-35; Lackner et al., 1985, J. Biol. Chem. 260(2):703-6; Hoeg et al., 1986, J. Biol. Chem. 261(9):3911-4; Gordon et al., 1984, J. Biol. Chem. 259(1):468-74; Powell et al., 1987, Cell 50(6):831-40; Aviram et al., 1998, Arterioscler. Thromb. Vasc. Biol. 18(10):1617-24; Aviram et al., 1998, J. Clin. Invest. 101(8):1581-90; Billecke et al., 2000, Drug Metab. Dispos. 28(11):1335-42; Draganov et al., 2000, J. Biol. Chem. 275(43):33435-42; Steinmetz and Utermann 1985, J. Biol. Chem. 260(4):2258-64; Widler et al., 1980, J. Biol. Chem. 255(21):10464-71; Dyer et al., 1995, J. Lipid Res. 36(1):80-8; Sorenson et al., 1999, Arterioscler. Thromb. Vasc. Biol. 19(9):2214-25; Palgunachari 1996, Arterioscler. Throb. Vasc. Biol. 16(2):328-38: Thurberg et al., J. Biol. Chem. 271(11):6062-70; Dyer 1991, J. Biol. Chem. 266(23):150009-15; Hill 1998, J. Biol. Chem. 273(47):30979-84).

Apolipoproteins utilized in the invention also include recombinant, synthetic, semi-synthetic or purified apolipoproteins. Methods for obtaining apolipoproteins or equivalents thereof, utilized by the invention are well-known in the art. For example, apolipoproteins can be separated from plasma or natural products by, for example, density gradient centrifugation or immunoaffinity chromatography, or produced synthetically, semi-synthetically or using recombinant DNA techniques known to those of the art (see, e.g., Mulugeta et al., 1998, J. Chromatogr. 798(1-2): 83-90; Chung et al., 1980, J. Lipid Res. 21(3):284-91; Cheung et al., 1987, J. Lipid Res. 28(8):913-29; Persson, et al., 1998, J. Chromatogr. 711:97-109; U.S. Pat. Nos. 5,059,528, 5,834,596, 5,876,968 and 5,721,114; and PCT Publications WO 86/04920 and WO 87/02062).

Apolipoproteins utilized in the invention further include apolipoprotein agonists such as peptides and peptide analogues that mimic the activity of ApoA-I, ApoA-I Milano (ApoA-I_(M)), ApoA-I Paris (ApoA-I_(P)), ApoA-II, ApoA-IV, and ApoE. For example, the apolipoprotein can be any of those described in U.S. Pat. Nos. 6,004,925, 6,037,323, 6,046,166, and 5,840,688, the contents of which are incorporated herein by reference in their entireties.

Apolipoprotein agonist peptides or peptide analogues can be synthesized or manufactured using any technique for peptide synthesis known in the art including, e.g., the techniques described in U.S. Pat. Nos. 6,004,925, 6,037,323 and 6,046,166. For example, the peptides may be prepared using the solid-phase synthetic technique initially described by Merrifield (1963, J. Am. Chem. Soc. 85:2149-2154). Other peptide synthesis techniques may be found in Bodanszky et al., Peptide Synthesis, John Wiley & Sons, 2d Ed., (1976) and other references readily available to those skilled in the art. A summary of polypeptide synthesis techniques can be found in Stuart and Young, Solid Phase Peptide. Synthesis, Pierce Chemical Company, Rockford, Ill., (1984). Peptides may also be synthesized by solution methods as described in The Proteins, Vol. II, 3d Ed., Neurath et al., Eds., p. 105-237, Academic Press, New York, N.Y. (1976). Appropriate protective groups for use in different peptide syntheses are described in the above-mentioned texts as well as in McOmie, Protective Groups in Organic Chemistry, Plenum Press, New York, N.Y. (1973). The peptides of the present invention might also be prepared by chemical or enzymatic cleavage from larger portions of, for example, apolipoprotein A-I.

In certain embodiments, the apolipoprotein can be a mixture of apolipoproteins. In one embodiment, the apolipoprotein can be a homogeneous mixture, that is, a single type of apolipoprotein. In another embodiment, the apolipoprotein can be a heterogeneous mixture of apolipoproteins, that is, a mixture of two or more different apolipoproteins. Embodiments of heterogenous mixtures of apolipoproteins can comprise, for example, a mixture of an apolipoprotein from an animal source and an apolipoprotein from a semi-synthetic source. In certain embodiments, a heterogenous mixture can comprise, for example, a mixture of ApoA-I and ApoA-I Milano. In certain embodiments, a heterogeneous mixture can comprise, for example, a mixture of ApoA-I Milano and ApoA-I Paris. Suitable mixtures for use in the methods and compositions of the invention will be apparent to one of skill in the art.

If the apolipoprotein is obtained from natural sources, it can be obtained from a plant or animal source. If the apolipoprotein is obtained from an animal source, the apolipoprotein can be from any species. In certain embodiments, the apolipoprotein can be obtained from an animal source. In certain embodiments, the apolipoprotein can be obtained from a human source. In preferred embodiments of the invention, the apolipoprotein is derived from the same species as the individual to which the apolipoprotein is administered.

Other Components

In numerous embodiments, amphipathic lipids are included in lipid particles of the invention. “Amphipathic lipids” refer to any suitable material, wherein the hydrophobic portion of the lipid material orients into a hydrophobic phase, while the hydrophilic portion orients toward the aqueous phase. Such compounds include, but are not limited to, phospholipids, aminolipids, and sphingolipids. Representative phospholipids include sphingomyelin, phosphatidylcholine, phosphatidylethanolamine, phosphatidylserine, phosphatidylinositol, phosphatidic acid, palmitoyloleoyl phosphatidylcholine, lysophosphatidylcholine, lysophosphatidylethanolamine, dipalmitoylphosphatidylcholine, dioleoylphosphatidylcholine, distearoylphosphatidylcholine, or dilinoleylphosphatidylcholine. Other phosphorus-lacking compounds, such as sphingolipids, glycosphingolipid families, diacylglycerols, and β-acyloxyacids, can also be used. Additionally, such amphipathic lipids can be readily mixed with other lipids, such as triglycerides and sterols.

Also suitable for inclusion in the lipid particles of the invention are programmable fusion lipids. Such lipid particles have little tendency to fuse with cell membranes and deliver their payload until a given signal event occurs. This allows the lipid particle to distribute more evenly after injection into an organism or disease site before it starts fusing with cells. The signal event can be, for example, a change in pH, temperature, ionic environment, or time. In the latter case, a fusion delaying or “cloaking” component, such as an ATTA-lipid conjugate or a PEG-lipid conjugate, can simply exchange out of the lipid particle membrane over time. Exemplary lipid anchors include those having lengths of from about C₁₄ to about C₂₂, preferably from about C₁₄ to about C₁₆. In some embodiments, a PEG moiety, for example an mPEG-NH₂, has a size of about 1000, 2000, 5000, 10,000, 15,000 or 20,000 daltons.

A lipid particle conjugated to a nucleic acid agent can also include a targeting moiety, e.g., a targeting moiety that is specific to a cell type or tissue. Targeting of lipid particles using a variety of targeting moieties, such as ligands, cell surface receptors, glycoproteins, vitamins (e.g., riboflavin) and monoclonal antibodies, has been previously described (see, e.g., U.S. Pat. Nos. 4,957,773 and 4,603,044). The targeting moieties can include the entire protein or fragments thereof. Targeting mechanisms generally require that the targeting agents be positioned on the surface of the lipid particle in such a manner that the targeting moiety is available for interaction with the target, for example, a cell surface receptor. A variety of different targeting agents and methods are known and available in the art, including those described, e.g., in Sapra, P. and Allen, T M, Prog. Lipid Res. 42(5):439-62 (2003); and Abra, R M et al., J. Liposome Res. 12:1-3, (2002).

The use of lipid particles, i.e., liposomes, with a surface coating of hydrophilic polymer chains, such as polyethylene glycol (PEG) chains, for targeting has been proposed (Allen, et al., Biochimica et Biophysica Acta 1237: 99-108 (1995); DeFrees, et al., Journal of the American Chemistry Society 118: 6101-6104 (1996); Blume, et al., Biochimica et Biophysica Acta 1149: 180-184 (1993); Klibanov, et al., Journal of Liposome Research 2: 321-334 (1992); U.S. Pat. No. 5,013,556; Zalipsky, Bioconjugate Chemistry 4: 296-299 (1993); Zalipsky, FEBS Letters 353: 71-74 (1994); Zalipsky, in Stealth Liposomes Chapter 9 (Lasic and Martin, Eds) CRC Press, Boca Raton Fla. (1995). In one approach, a ligand, such as an antibody, for targeting the lipid particle is linked to the polar head group of lipids forming the lipid particle. In another approach, the targeting ligand is attached to the distal ends of the PEG chains forming the hydrophilic polymer coating (Klibanov, et al., Journal of Liposome Research 2: 321-334 (1992); Kirpotin et al., FEBS Letters 388: 115-118 (1996)).

Standard methods for coupling the target agents can be used. For example, phosphatidylethanolamine, which can be activated for attachment of target agents, or derivatized lipophilic compounds, such as lipid-derivatized bleomycin, can be used. Antibody-targeted liposomes can be constructed using, for instance, liposomes that incorporate protein A (see, Renneisen, et al., J. Bio. Chem., 265:16337-16342 (1990) and Leonetti, et al., Proc. Natl. Acad. Sci. (USA), 87:2448-2451 (1990). Other examples of antibody conjugation are disclosed in U.S. Pat. No. 6,027,726, the teachings of which are incorporated herein by reference. Examples of targeting moieties can also include other proteins, specific to cellular components, including antigens associated with neoplasms or tumors. Proteins used as targeting moieties can be attached to the liposomes via covalent bonds (see, Heath, Covalent Attachment of Proteins to Liposomes, 149 Methods in Enzymology 111-119 (Academic Press, Inc. 1987)). Other targeting methods include the biotin-avidin system.

Production of Nucleic Acid-Lipid Particles

In one embodiment, the nucleic acid-lipid particle formulations of the invention are produced via an extrusion method or an in-line mixing method.

The extrusion method (also refer to as preformed method or batch process) is a method where the empty liposomes (i.e. no nucleic acid) are prepared first, followed by the addition of nucleic acid to the empty liposome. Extrusion of liposome compositions through a small-pore polycarbonate membrane or an asymmetric ceramic membrane results in a relatively well-defined size distribution. Typically, the suspension is cycled through the membrane one or more times until the desired liposome complex size distribution is achieved. The liposomes may be extruded through successively smaller-pore membranes, to achieve a gradual reduction in liposome size. In some instances, the lipid-nucleic acid compositions which are formed can be used without any sizing. These methods are disclosed in the U.S. Pat. No. 5,008,050; U.S. Pat. No. 4,927,637; U.S. Pat. No. 4,737,323; Biochim Biophys Acta. 1979 Oct. 19; 557(1):9-23; Biochim Biophys Acta. 1980 Oct. 2; 601(3):559-7; Biochim Biophys Acta. 1986 Jun. 13; 858(1):161-8; and Biochim. Biophys. Acta 1985 812, 55-65, which are hereby incorporated by reference in their entirety.

The in-line mixing method is a method wherein both the lipids and the nucleic acid are added in parallel into a mixing chamber. The mixing chamber can be a simple T-connector or any other mixing chamber that is known to one skill in the art. These methods are disclosed in U.S. Pat. No. 6,534,018 and U.S. Pat. No. 6,855,277; US publication 2007/0042031 and Pharmaceuticals Research, Vol. 22, No. 3, March 2005, p. 362-372, which are hereby incorporated by reference in their entirety.

It is further understood that the formulations of the invention can be prepared by any methods known to one of ordinary skill in the art.

Characterization of Nucleic Acid-Lipid Particles

Formulations prepared by either the standard or extrusion-free method can be characterized in similar manners. For example, formulations are typically characterized by visual inspection. They should be whitish translucent solutions free from aggregates or sediment. Particle size and particle size distribution of lipid-nanoparticles can be measured by light scattering using, for example, a Malvern Zetasizer Nano ZS (Malvern, USA). Particles should be about 20-300 nm, such as 40-100 nm in size. The particle size distribution should be unimodal. The total siRNA concentration in the formulation, as well as the entrapped fraction, is estimated using a dye exclusion assay. A sample of the formulated siRNA can be incubated with an RNA-binding dye, such as Ribogreen (Molecular Probes) in the presence or absence of a formulation disrupting surfactant, e.g., 0.5% Triton-X100. The total siRNA in the formulation can be determined by the signal from the sample containing the surfactant, relative to a standard curve. The entrapped fraction is determined by subtracting the “free” siRNA content (as measured by the signal in the absence of surfactant) from the total siRNA content. Percent entrapped siRNA is typically >85%. In one embodiment, the formulations of the invention are entrapped by at least 75%, at least 80% or at least 90%.

For nucleic acid-lipid particle formulations, the particle size is at least 30 nm, at least 40 nm, at least 50 nm, at least 60 nm, at least 70 nm, at least 80 nm, at least 90 nm, at least 100 nm, at least 110 nm, and at least 120 nm. The suitable range is typically about at least 50 nm to about at least 110 nm, about at least 60 nm to about at least 100 nm, or about at least 80 nm to about at least 90 nm.

Formulations of Nucleic Acid-Lipid Particles

LNP01

One example of synthesis of a nucleic acid-lipid particle is as follows. Nucleic acid-lipid particles are synthesized using the lipidoid ND98.4HCl (MW 1487) (Formula 1), Cholesterol (Sigma-Aldrich), and PEG-Ceramide C16 (Avanti Polar Lipids). This nucleic acid-lipid particle is sometimes referred to as a LNP01 particles. Stock solutions of each in ethanol can be prepared as follows: ND98, 133 mg/ml; Cholesterol, 25 mg/ml, PEG-Ceramide C16, 100 mg/ml. The ND98, Cholesterol, and PEG-Ceramide C16 stock solutions can then be combined in a, e.g., 42:48:10 molar ratio. The combined lipid solution can be mixed with aqueous siRNA (e.g., in sodium acetate pH 5) such that the final ethanol concentration is about 35-45% and the final sodium acetate concentration is about 100-300 mM. Lipid-siRNA nanoparticles typically form spontaneously upon mixing. Depending on the desired particle size distribution, the resultant nanoparticle mixture can be extruded through a polycarbonate membrane (e.g., 100 nm cut-off) using, for example, a thermobarrel extruder, such as Lipex Extruder (Northern Lipids, Inc). In some cases, the extrusion step can be omitted. Ethanol removal and simultaneous buffer exchange can be accomplished by, for example, dialysis or tangential flow filtration. Buffer can be exchanged with, for example, phosphate buffered saline (PBS) at about pH 7, e.g., about pH 6.9, about pH 7.0, about pH 7.1, about pH 7.2, about pH 7.3, or about pH 7.4.

LNP01 formulations are described, e.g., in International Application Publication No. WO 2008/042973, which is hereby incorporated by reference.

Additional exemplary nucleic acid-lipid particle formulations are described in the following table. It is to be understood that the name of the nucleic acid-lipid particle in the table is not meant to be limiting. For example, as used herein, the term SNALP refers to formulations that include the cationic lipid DLinDMA.

cationic lipid/non-cationic lipid/cholesterol/PEG-lipid conjugate mol % ratio Name Lipid:siRNA ratio SNALP DLinDMA/DPPC/Cholesterol/PEG-cDMA (57.1/7.1/34.4/1.4) lipid:siRNA ~7:1 LNP- XTC/DPPC/Cholesterol/PEG-cDMA S-X 57.1/7.1/34.4/1.4 lipid:siRNA ~7:1 LNP05 XTC/DSPC/Cholesterol/PEG-DMG 57.5/7.5/31.5/3.5 lipid:siRNA ~6:1 LNP06 XTC/DSPC/Cholesterol/PEG-DMG 57.5/7.5/31.5/3.5 lipid:siRNA ~11:1 LNP07 XTC/DSPC/Cholesterol/PEG-DMG 60/7.5/31/1.5, lipid:siRNA ~6:1 LNP08 XTC/DSPC/Cholesterol/PEG-DMG 60/7.5/31/1.5, lipid:siRNA ~11:1 LNP09 XTC/DSPC/Cholesterol/PEG-DMG 50/10/38.5/1.5 lipid:siRNA ~10:1 LNP10 ALNY-100/DSPC/Cholesterol/PEG-DMG 50/10/38.5/1.5 lipid:siRNA ~10:1 LNP11 MC3/DSPC/Cholesterol/PEG-DMG 50/10/38.5/1.5 lipid:siRNA ~10:1 LNP13 XTC/DSPC/Cholesterol/PEG-DMG 50/10/38.5/1.5 lipid:siRNA ~33:1 LNP14 MC3/DSPC/Cholesterol/PEG-DMG 40/15/40/5 lipid:siRNA ~11:1 LNP15 MC3/DSPC/Cholesterol/PEG-DSG/GalNAc-PEG-DSG 50/10/35/4.5/0.5 lipid:siRNA ~11:1 LNP16 MC3/DSPC/Cholesterol/PEG-DMG 50/10/38.5/1.5 lipid:siRNA ~7:1 LNP17 MC3/DSPC/Choleslerol/PEG-DSG 50/10/38.5/1.5 lipid:siRNA ~10:1 LNP18 MC3/DSPC/Cholesterol/PEG-DMG 50/10/38.5/1.5 lipid:siRNA ~12:1 LNP19 MC3/DSPC/Cholesterol/PEG-DMG 50/10/35/5 lipid:siRNA ~8:1 LNP20 MC3/DSPC/Cholesterol/PEG-DPG 50/10/38.5/1.5 lipid:siRNA ~10:1 LNP22 XTC/DSPC/Choleslerol/PEG-DSG 50/10/38.5/1.5 lipid:siRNA ~10:1

XTC comprising formulations are described, e.g., in PCT/US10/22614 filed on Jan. 29, 2010, which is hereby incorporated by reference.

MC3 comprising formulations are described, e.g., in U.S. Ser. No. 12/813,448, filed Jun. 10, 2010, and PCT/US10/38224, filed Jun. 10, 2010, which is hereby incorporated by reference.

ALNY-100 comprising formulations are described, e.g., International patent application number PCT/US09/63933, filed on Nov. 10, 2009, which is hereby incorporated by reference.

TechG1 (also known as C12-200) comprising formulations are described, e.g., International patent application number PCT/US10/33777, filed on May 15, 2010, which is hereby incorporated by reference. An embodiment of TechG1 is shown below.

Additional representative formulations delineated in Tables A and B. Lipid refers to a cationic lipid.

TABLE A Composition of exemplary nucleic acid-lipid particle (mole %) prepared via extrusion methods. Lipid DSPC (mol %)  (mol %) Chol (mol %) PEG (mol %) Lipid/siRNA 20 30 40 10 2.13 20 30 40 10 2.35 20 30 40 10 2.37 20 30 40 10 3.23 20 30 40 10 3.91 30 20 40 10 2.89 30 20 40 10 3.34 30 20 40 10 3.34 30 20 40 10 4.10 30 20 40 10 5.64 40 10 40 10 3.02 40 10 40 10 3.35 40 10 40 10 3.74 40 10 40 10 5.80 40 10 40 10 8.00 45 5 40 10 3.27 45 5 40 10 3.30 45 5 40 10 4.45 45 5 40 10 7.00 45 5 40 10 9.80 50 0 40 10 27.03 20 35 40 5 3.00 20 35 40 5 3.32 20 35 40 5 3.05 20 35 40 5 3.67 20 35 40 5 4.71 30 25 40 5 2.47 30 25 40 5 2.98 30 25 40 5 3.29 30 25 40 5 4.99 30 25 40 5 7.15 40 15 40 5 2.79 40 15 40 5 3.29 40 15 40 5 4.33 40 15 40 5 7.05 40 15 40 5 9.63 45 10 40 5 2.44 45 10 40 5 3.21 45 10 40 5 4.29 45 10 40 5 6.50 45 10 40 5 8.67 20 35 40 5 4.10 20 35 40 5 4.83 30 25 40 5 3.86 30 25 40 5 5.38 30 25 40 5 7.07 40 15 40 5 3.85 40 15 40 5 4.88 40 15 40 5 7.22 40 15 40 5 9.75 45 10 40 5 2.83 45 10 40 5 3.85 45 10 40 5 4.88 45 10 40 5 7.05 45 10 40 5 9.29 45 20 30 5 4.01 45 20 30 5 3.70 50 15 30 5 4.75 50 15 30 5 3.80 55 10 30 5 3.85 55 10 30 5 4.13 60 5 30 5 5.09 60 5 30 5 4.67 65 0 30 5 4.75 65 0 30 5 6.06 56.5 10 30 3.5 3.70 56.5 10 30 3.5 3.56 57.5 10 30 2.5 3.48 57.5 10 30 2.5 3.20 58.5 10 30 1.5 3.24 58.5 10 30 1.5 3.13 59.5 10 30 0.5 3.24 59.5 10 30 0.5 3.03 45 10 40 5 7.57 45 10 40 5 7.24 45 10 40 5 7.48 45 10 40 5 7.84 65 0 30 5 4.01 60 5 30 5 3.70 55 10 30 5 3.65 50 10 35 5 3.43 50 15 30 5 3.80 45 15 35 5 3.70 45 20 30 5 3.75 45 25 25 5 3.85 55 10 32.5 2.5 3.61 60 10 27.5 2.5 3.65 60 10 25 5 4.07 55 5 38.5 1.5 3.75 60 10 28.5 1.5 3.43 55 10 33.5 1.5 3.48 60 5 33.5 1.5 3.43 55 5 37.5 2.5 3.75 60 5 32.5 2.5 4.52 60 5 32.5 2.5 3.52 45 15 (DMPC) 35 5 3.20 45 15 (DPPC) 35 5 3.43 45 15 (DOPC) 35 5 4.52 45 15 (POPC) 35 5 3.85 55 5 37.5 2.5 3.96 55 10 32.5 2.5 3.56 60 5 32.5 2.5 3.80 60 10 27.5 2.5 3.75 60 5 30 5 4.19 60 5 33.5 1.5 3.48 60 5 33.5 1.5 6.64 60 5 30 5 3.90 60 5 30 5 4.65 60 5 30 5 5.88 60 5 30 5 7.51 60 5 30 5 9.51 60 5 30 5 11.06 62.5 2.5 50 5 6.63 45 15 35 5 3.31 45 15 35 5 6.80 60 5 25 10 6.48 60 5 32.5 2.5 3.43 60 5 30 5 3.90 60 5 30 5 7.61 45 15 35 5 3.13 45 15 35 5 6.42 60 5 25 10 6.48 60 5 32.5 2.5 3.03 60 5 30 5 3.43 60 5 30 5 6.72 60 5 30 5 4.13 70 5 20 5 5.48 80 5 10 5 5.94 90 5 0 5 9.50 60 5 30 5 C12PEG 3.85 60 5 30 5 3.70 60 5 30 5 C16PEG 3.80 60 5 30 5 4.19 60 5 29 5 4.07 60 5 30 5 3.56 60 5 30 5 3.39 60 5 30 5 3.96 60 5 30 5 4.01 60 5 30 5 4.07 60 5 30 5 4.25 60 5 30 5 3.80 60 5 30 5 3.31 60 5 30 5 4.83 60 5 30 5 4.67 60 5 30 5 3.96 57.5 7.5 33.5 1.5 3.39 57.5 7.5 32.5 2.5 3.39 57.5 7.5 31.5 3.5 3.52 57.5 7.5 30 5 4.19 60 5 30 5 3.96 60 5 30 5 3.96 60 5 30 5 3.56 60 5 33.5 1.5 3.52 60 5 25 10 5.18 60 5 (DPPC) 30 5 4.25 60 5 32.5 2.5 3.70 57.5 7.5 31.5 3.5 3.06 57.5 7.5 31.5 3.5 3.65 57.5 7.5 31.5 3.5 4.70 57.5 7.5 31.5 3.5 6.56

TABLE B Composition of exemplary nucleic acid-lipid particles prepared via in-line mixing Lipid DSPC (mol %) (mol %) Chol (mol %) PEG (mol %) Lipid A/siRNA 55 5 37.5 2.5 3.96 55 10 32.5 2.5 3.56 60 5 32.5 2.5 3.80 60 10 27.5 2.5 3.75 60 5 30 5 4.19 60 5 33.5 1.5 3.48 60 5 33.5 1.5 6.64 60 5 25 10 6.79 60 5 32.5 2.5 3.96 60 5 34 1 3.75 60 5 34.5 0.5 3.28 50 5 40 5 3.96 60 5 30 5 4.75 70 5 20 5 5.00 80 5 10 5 5.18 60 5 30 5 13.60 60 5 30 5 14.51 60 5 30 5 6.20 60 5 30 5 4.60 60 5 30 5 6.20 60 5 30 5 5.82 40 5 54 1 3.39 40 7.5 51.5 1 3.39 40 10 49 1 3.39 50 5 44 1 3.39 50 7.5 41.5 1 3.43 50 10 39 1 3.35 60 5 34 1 3.52 60 7.5 31.5 1 3.56 60 10 29 1 3.80 70 5 24 1 3.70 70 7.5 21.5 1 4.13 70 10 19 1 3.85 60 5 34 1 3.52 60 5 34 1 3.70 60 5 34 1 3.52 60 7.5 27.5 5 5.18 60 7.5 29 3.5 4.45 60 5 31.5 3.5 4.83 60 7.5 31 1.5 3.48 57.5 7.5 30 5 4.75 57.5 7.5 31.5 3.5 4.83 57.5 5 34 3.5 4.67 57.5 7.5 33.5 1.5 3.43 55 7.5 32.5 5 4.38 55 7.5 34 3.5 4.13 55 5 36.5 3.5 4.38 55 7.5 36 1.5 3.35

Synthesis of Cationic Lipids.

Any of the compounds, e.g., cationic lipids and the like, used in the nucleic acid-lipid particles of the invention may be prepared by known organic synthesis techniques, including the methods described in more detail in the Examples. All substituents are as defined below unless indicated otherwise.

“Alkyl” means a straight chain or branched, noncyclic or cyclic, saturated aliphatic hydrocarbon containing from 1 to 24 carbon atoms. Representative saturated straight chain alkyls include methyl, ethyl, n-propyl, n-butyl, n-pentyl, n-hexyl, and the like; while saturated branched alkyls include isopropyl, sec-butyl, isobutyl, tert-butyl, isopentyl, and the like. Representative saturated cyclic alkyls include cyclopropyl, cyclobutyl, cyclopentyl, cyclohexyl, and the like; while unsaturated cyclic alkyls include cyclopentenyl and cyclohexenyl, and the like.

“Alkenyl” means an alkyl, as defined above, containing at least one double bond between adjacent carbon atoms. Alkenyls include both cis and trans isomers. Representative straight chain and branched alkenyls include ethylenyl, propylenyl, 1-butenyl, 2-butenyl, isobutylenyl, 1-pentenyl, 2-pentenyl, 3-methyl-1-butenyl, 2-methyl-2-butenyl, 2,3-dimethyl-2-butenyl, and the like.

“Alkynyl” means any alkyl or alkenyl, as defined above, which additionally contains at least one triple bond between adjacent carbons. Representative straight chain and branched alkynyls include acetylenyl, propynyl, 1-butynyl, 2-butynyl, 1-pentynyl, 2-pentynyl, 3-methyl-1 butynyl, and the like.

“Acyl” means any alkyl, alkenyl, or alkynyl wherein the carbon at the point of attachment is substituted with an oxo group, as defined below. For example, —C(═O)alkyl, —C(═O)alkenyl, and —C(═O)alkynyl are acyl groups.

“Heterocycle” means a 5- to 7-membered monocyclic, or 7- to 10-membered bicyclic, heterocyclic ring which is either saturated, unsaturated, or aromatic, and which contains from 1 or 2 heteroatoms independently selected from nitrogen, oxygen and sulfur, and wherein the nitrogen and sulfur heteroatoms may be optionally oxidized, and the nitrogen heteroatom may be optionally quaternized, including bicyclic rings in which any of the above heterocycles are fused to a benzene ring. The heterocycle may be attached via any heteroatom or carbon atom. Heterocycles include heteroaryls as defined below. Heterocycles include morpholinyl, pyrrolidinonyl, pyrrolidinyl, piperidinyl, piperizynyl, hydantoinyl, valerolactamyl, oxiranyl, oxetanyl, tetrahydrofuranyl, tetrahydropyranyl, tetrahydropyridinyl, tetrahydroprimidinyl, tetrahydrothiophenyl, tetrahydrothiopyranyl, tetrahydropyrimidinyl, tetrahydrothiophenyl, tetrahydrothiopyranyl, and the like.

The terms “optionally substituted alkyl”, “optionally substituted alkenyl”, “optionally substituted alkynyl”, “optionally substituted acyl”, and “optionally substituted heterocycle” means that, when substituted, at least one hydrogen atom is replaced with a substituent. In the case of an oxo substituent (═O) two hydrogen atoms are replaced. In this regard, substituents include oxo, halogen, heterocycle, —CN, —OR^(x), —R^(x)R^(y), —NR^(x)C(═O)R^(y), —NR^(x)SO₂R^(y), —C(═O)R^(x), —C(═O)OR^(x), —C(═O)NR^(x)R^(y), —SO_(n)R^(x) and —SO_(n)NR^(x)R^(y), wherein n is 0, 1 or 2, R^(x) and R^(y) are the same or different and independently hydrogen, alkyl or heterocycle, and each of said alkyl and heterocycle substituents may be further substituted with one or more of oxo, halogen, —OH, —CN, alkyl, —OR^(x), heterocycle, —NR^(x)R^(y), —NR^(x)C(═O)R^(y), —NR^(x)SO₂R^(y), —C(═O)R^(x), —C(═O)OR^(x), —C(═O)NR^(x)R^(y), —SO_(n)R^(x) and —SO_(n)NR^(x)R^(y).

“Halogen” means fluoro, chloro, bromo and iodo.

In some embodiments, the methods of the invention may require the use of protecting groups. Protecting group methodology is well known to those skilled in the art (see, for example, PROTECTIVE GROUPS IN ORGANIC SYNTHESIS, Green, T. W. et al., Wiley-Interscience, New York City, 1999). Briefly, protecting groups within the context of this invention are any group that reduces or eliminates unwanted reactivity of a functional group. A protecting group can be added to a functional group to mask its reactivity during certain reactions and then removed to reveal the original functional group. In some embodiments an “alcohol protecting group” is used. An “alcohol protecting group” is any group which decreases or eliminates unwanted reactivity of an alcohol functional group. Protecting groups can be added and removed using techniques well known in the art.

Synthesis of Formula A

In one embodiments, nucleic acid-lipid particles of the invention are formulated using a cationic lipid of formula A:

where R1 and R2 are independently alkyl, alkenyl or alkynyl, each can be optionally substituted, and R3 and R4 are independently lower alkyl or R3 and R4 can be taken together to form an optionally substituted heterocyclic ring. In some embodiments, the cationic lipid is XTC (2,2-Dilinoleyl-4-dimethylaminoethyl-[1,3]-dioxolane). In general, the lipid of formula A above may be made by the following Reaction Schemes 1 or 2, wherein all substituents are as defined above unless indicated otherwise.

Lipid A, where R₁ and R₂ are independently alkyl, alkenyl or alkynyl, each can be optionally substituted, and R₃ and R₄ are independently lower alkyl or R₃ and R₄ can be taken together to form an optionally substituted heterocyclic ring, can be prepared according to Scheme 1. Ketone 1 and bromide 2 can be purchased or prepared according to methods known to those of ordinary skill in the art. Reaction of 1 and 2 yields ketal 3. Treatment of ketal 3 with amine 4 yields lipids of formula A. The lipids of formula A can be converted to the corresponding ammonium salt with an organic salt of formula 5, where X is anion counter ion selected from halogen, hydroxide, phosphate, sulfate, or the like.

Alternatively, the ketone 1 starting material can be prepared according to Scheme 2. Grignard reagent 6 and cyanide 7 can be purchased or prepared according to methods known to those of ordinary skill in the art. Reaction of 6 and 7 yields ketone 1. Conversion of ketone 1 to the corresponding lipids of formula A is as described in Scheme 1.

Synthesis of MC3

Preparation of DLin-M-C3-DMA (i.e., (6Z,9Z,28Z,31Z)-heptatriaconta-6,9,28,31-tetraen-19-yl 4-(dimethylamino)butanoate) was as follows. A solution of (6Z,9Z,28Z,31Z)-heptatriaconta-6,9,28,31-tetraen-19-ol (0.53 g), 4-N,N-dimethylaminobutyric acid hydrochloride (0.51 g), 4-N,N-dimethylaminopyridine (0.61 g) and 1-ethyl-3-(3-dimethylaminopropyl)carbodiimide hydrochloride (0.53 g) in dichloromethane (5 mL) was stirred at room temperature overnight. The solution was washed with dilute hydrochloric acid followed by dilute aqueous sodium bicarbonate. The organic fractions were dried over anhydrous magnesium sulphate, filtered and the solvent removed on a rotovap. The residue was passed down a silica gel column (20 g) using a 1-5% methanol/dichloromethane elution gradient. Fractions containing the purified product were combined and the solvent removed, yielding a colorless oil (0.54 g).

Synthesis of ALNY-100

Synthesis of ketal 519 [ALNY-100] was performed using the following scheme 3:

Synthesis of 515:

To a stirred suspension of LiAlH4 (3.74 g, 0.09852 mol) in 200 ml anhydrous THF in a two neck RBF (1 L), was added a solution of 514 (10 g, 0.04926 mol) in 70 mL of THF slowly at 0° C. under nitrogen atmosphere. After complete addition, reaction mixture was warmed to room temperature and then heated to reflux for 4 h. Progress of the reaction was monitored by TLC. After completion of reaction (by TLC) the mixture was cooled to 0° C. and quenched with careful addition of saturated Na2SO4 solution. Reaction mixture was stirred for 4 h at room temperature and filtered off. Residue was washed well with THF. The filtrate and washings were mixed and diluted with 400 mL dioxane and 26 mL conc. HCl and stirred for 20 minutes at room temperature. The volatilities were stripped off under vacuum to furnish the hydrochloride salt of 515 as a white solid. Yield: 7.12 g 1H-NMR (DMSO, 400 MHz): δ=9.34 (broad, 2H), 5.68 (s, 2H), 3.74 (m, 1H), 2.66-2.60 (m, 2H), 2.50-2.45 (m, 5H).

Synthesis of 516:

To a stirred solution of compound 515 in 100 mL dry DCM in a 250 mL two neck RBF, was added NEt3 (37.2 mL, 0.2669 mol) and cooled to 0° C. under nitrogen atmosphere. After a slow addition of N-(benzyloxy-carbonyloxy)-succinimide (20 g, 0.08007 mol) in 50 mL dry DCM, reaction mixture was allowed to warm to room temperature. After completion of the reaction (2-3 h by TLC) mixture was washed successively with 1N HCl solution (1×100 mL) and saturated NaHCO3 solution (1×50 mL). The organic layer was then dried over anhyd. Na2SO4 and the solvent was evaporated to give crude material which was purified by silica gel column chromatography to get 516 as sticky mass. Yield: 11 g (89%). 1H-NMR (CDCl3, 400 MHz): δ=7.36-7.27 (m, 5H), 5.69 (s, 2H), 5.12 (s, 2H), 4.96 (br., 1H) 2.74 (s, 3H), 2.60 (m, 2H), 2.30-2.25 (m, 2H). LC-MS [M+H]− 232.3 (96.94%).

Synthesis of 517A and 517B:

The cyclopentene 516 (5 g, 0.02164 mol) was dissolved in a solution of 220 mL acetone and water (10:1) in a single neck 500 mL RBF and to it was added N-methyl morpholine-N-oxide (7.6 g, 0.06492 mol) followed by 4.2 mL of 7.6% solution of OsO4 (0.275 g, 0.00108 mol) in tert-butanol at room temperature. After completion of the reaction (˜3 h), the mixture was quenched with addition of solid Na2SO3 and resulting mixture was stirred for 1.5 h at room temperature. Reaction mixture was diluted with DCM (300 mL) and washed with water (2×100 mL) followed by saturated NaHCO3 (1×50 mL) solution, water (1×30 mL) and finally with brine (1×50 mL). Organic phase was dried over an.Na2SO4 and solvent was removed in vacuum. Silica gel column chromatographic purification of the crude material was afforded a mixture of diastereomers, which were separated by prep HPLC. Yield: —6 g crude

517A—Peak-1 (white solid), 5.13 g (96%). 1H-NMR (DMSO, 400 MHz): δ=7.39-7.31 (m, 5H), 5.04 (s, 2H), 4.78-4.73 (m, 1H), 4.48-4.47 (d, 2H), 3.94-3.93 (m, 2H), 2.71 (s, 3H), 1.72-1.67 (m, 4H). LC-MS—[M+H]− 266.3, [M+NH4+]− 283.5 present, HPLC-97.86%. Stereochemistry confirmed by X-ray.

Synthesis of 518:

Using a procedure analogous to that described for the synthesis of compound 505, compound 518 (1.2 g, 41%) was obtained as a colorless oil. 1H-NMR (CDCl3, 400 MHz): δ=7.35-7.33 (m, 4H), 7.30-7.27 (m, 1H), 5.37-5.27 (m, 8H), 5.12 (s, 2H), 4.75 (m, 1H), 4.58-4.57 (m, 2H), 2.78-2.74 (m, 7H), 2.06-2.00 (m, 8H), 1.96-1.91 (m, 2H), 1.62 (m, 4H), 1.48 (m, 2H), 1.37-1.25 (br m, 36H), 0.87 (m, 6H). HPLC-98.65%.

General Procedure for the Synthesis of Compound 519:

A solution of compound 518 (1 eq) in hexane (15 mL) was added in a drop-wise fashion to an ice-cold solution of LAH in THF (1 M, 2 eq). After complete addition, the mixture was heated at 40° C. over 0.5 h then cooled again on an ice bath. The mixture was carefully hydrolyzed with saturated aqueous Na2SO4 then filtered through celite and reduced to an oil. Column chromatography provided the pure 519 (1.3 g, 68%) which was obtained as a colorless oil. 13C NMR=130.2, 130.1 (×2), 127.9 (×3), 112.3, 79.3, 64.4, 44.7, 38.3, 35.4, 31.5, 29.9 (×2), 29.7, 29.6 (×2), 29.5 (×3), 29.3 (×2), 27.2 (×3), 25.6, 24.5, 23.3, 226, 14.1; Electrospray MS (+ve): Molecular weight for C44H80NO2 (M+H)+ Calc. 654.6, Found 654.6.

Therapeutic Agent-Lipid Particle Compositions and Formulations

The invention includes compositions comprising a lipid particle of the invention and an active agent, wherein the active agent is associated with the lipid particle. In particular embodiments, the active agent is a therapeutic agent. In particular embodiments, the active agent is encapsulated within an aqueous interior of the lipid particle. In other embodiments, the active agent is present within one or more lipid layers of the lipid particle. In other embodiments, the active agent is bound to the exterior or interior lipid surface of a lipid particle.

“Fully encapsulated” as used herein indicates that the nucleic acid in the particles is not significantly degraded after exposure to serum or a nuclease assay that would significantly degrade free DNA. In a fully encapsulated system, preferably less than 25% of particle nucleic acid is degraded in a treatment that would normally degrade 100% of free nucleic acid, more preferably less than 10% and most preferably less than 5% of the particle nucleic acid is degraded. Alternatively, full encapsulation may be determined by an Oligreen® assay. Oligreen® is an ultra-sensitive fluorescent nucleic acid stain for quantitating oligonucleotides and single-stranded DNA in solution (available from Invitrogen Corporation, Carlsbad, Calif.). Fully encapsulated also suggests that the particles are serum stable, that is, that they do not rapidly decompose into their component parts upon in vivo administration.

Active agents, as used herein, include any molecule or compound capable of exerting a desired effect on a cell, tissue, organ, or subject. Such effects may be biological, physiological, or cosmetic, for example. Active agents may be any type of molecule or compound, including e.g., nucleic acids, peptides and polypeptides, including, e.g., antibodies, such as, e.g., polyclonal antibodies, monoclonal antibodies, antibody fragments; humanized antibodies, recombinant antibodies, recombinant human antibodies, and Primatized™ antibodies, cytokines, growth factors, apoptotic factors, differentiation-inducing factors, cell surface receptors and their ligands; hormones; and small molecules, including small organic molecules or compounds.

In one embodiment, the active agent is a therapeutic agent, or a salt or derivative thereof. Therapeutic agent derivatives may be therapeutically active themselves or they may be prodrugs, which become active upon further modification. Thus, in one embodiment, a therapeutic agent derivative retains some or all of the therapeutic activity as compared to the unmodified agent, while in another embodiment, a therapeutic agent derivative lacks therapeutic activity.

In various embodiments, therapeutic agents include any therapeutically effective agent or drug, such as anti-inflammatory compounds, anti-depressants, stimulants, analgesics, antibiotics, birth control medication, antipyretics, vasodilators, anti-angiogenics, cytovascular agents, signal transduction inhibitors, cardiovascular drugs, e.g., anti-arrhythmic agents, vasoconstrictors, hormones, and steroids. In certain embodiments, the therapeutic agent is an oncology drug, which may also be referred to as an anti-tumor drug, an anti-cancer drug, a tumor drug, an antineoplastic agent, or the like.

Additional Formulations

Emulsions

The compositions of the present invention may be prepared and formulated as emulsions. Emulsions are typically heterogeneous systems of one liquid dispersed in another in the form of droplets usually exceeding 0.1 μm in diameter (Idson, in Pharmaceutical Dosage Forms, Lieberman, Rieger and Banker (Eds.), 1988, Marcel Dekker, Inc., New York, N.Y., volume 1, p. 199; Rosoff, in Pharmaceutical Dosage Forms, Lieberman, Rieger and Banker (Eds.), 1988, Marcel Dekker, Inc., New York, N.Y., Volume 1, p. 245; Block in Pharmaceutical Dosage Forms, Lieberman, Rieger and Banker (Eds.), 1988, Marcel Dekker, Inc., New York, N.Y., volume 2, p. 335; Higuchi et al., in Remington's Pharmaceutical Sciences, Mack Publishing Co., Easton, Pa., 1985, p. 301). Emulsions are often biphasic systems comprising two immiscible liquid phases intimately mixed and dispersed with each other. In general, emulsions may be of either the water-in-oil (w/o) or the oil-in-water (o/w) variety. When an aqueous phase is finely divided into and dispersed as minute droplets into a bulk oily phase, the resulting composition is called a water-in-oil (w/o) emulsion. Alternatively, when an oily phase is finely divided into and dispersed as minute droplets into a bulk aqueous phase, the resulting composition is called an oil-in-water (o/w) emulsion. Emulsions may contain additional components in addition to the dispersed phases, and the active drug which may be present as a solution in either the aqueous phase, oily phase or itself as a separate phase. Pharmaceutical excipients such as emulsifiers, stabilizers, dyes, and anti-oxidants may also be present in emulsions as needed. Pharmaceutical emulsions may also be multiple emulsions that are comprised of more than two phases such as, for example, in the case of oil-in-water-in-oil (o/w/o) and water-in-oil-in-water (w/o/w) emulsions. Such complex formulations often provide certain advantages that simple binary emulsions do not. Multiple emulsions in which individual oil droplets of an o/w emulsion enclose small water droplets constitute a w/o/w emulsion. Likewise a system of oil droplets enclosed in globules of water stabilized in an oily continuous phase provides an o/w/o emulsion.

Emulsions are characterized by little or no thermodynamic stability. Often, the dispersed or discontinuous phase of the emulsion is well dispersed into the external or continuous phase and maintained in this form through the means of emulsifiers or the viscosity of the formulation. Either of the phases of the emulsion may be a semisolid or a solid, as is the case of emulsion-style ointment bases and creams. Other means of stabilizing emulsions entail the use of emulsifiers that may be incorporated into either phase of the emulsion. Emulsifiers may broadly be classified into four categories: synthetic surfactants, naturally occurring emulsifiers, absorption bases, and finely dispersed solids (Idson, in Pharmaceutical Dosage Forms, Lieberman, Rieger and Banker (Eds.), 1988, Marcel Dekker, Inc., New York, N.Y., volume 1, p. 199).

Synthetic surfactants, also known as surface active agents, have found wide applicability in the formulation of emulsions and have been reviewed in the literature (Rieger, in Pharmaceutical Dosage Forms, Lieberman, Rieger and Banker (Eds.), 1988, Marcel Dekker, Inc., New York, N.Y., volume 1, p. 285; Idson, in Pharmaceutical Dosage Forms, Lieberman, Rieger and Banker (Eds.), Marcel Dekker, Inc., New York, N.Y., 1988, volume 1, p. 199). Surfactants are typically amphiphilic and comprise a hydrophilic and a hydrophobic portion. The ratio of the hydrophilic to the hydrophobic nature of the surfactant has been termed the hydrophile/lipophile balance (HLB) and is a valuable tool in categorizing and selecting surfactants in the preparation of formulations. Surfactants may be classified into different classes based on the nature of the hydrophilic group: nonionic, anionic, cationic and amphoteric (Rieger, in Pharmaceutical Dosage Forms, Lieberman, Rieger and Banker (Eds.), 1988, Marcel Dekker, Inc., New York, N.Y., volume 1, p. 285).

Naturally occurring emulsifiers used in emulsion formulations include lanolin, beeswax, phosphatides, lecithin and acacia. Absorption bases possess hydrophilic properties such that they can soak up water to form w/o emulsions yet retain their semisolid consistencies, such as anhydrous lanolin and hydrophilic petrolatum. Finely divided solids have also been used as good emulsifiers especially in combination with surfactants and in viscous preparations. These include polar inorganic solids, such as heavy metal hydroxides, non-swelling clays such as bentonite, attapulgite, hectorite, kaolin, montmorillonite, colloidal aluminum silicate and colloidal magnesium aluminum silicate, pigments and nonpolar solids such as carbon or glyceryl tristearate.

A large variety of non-emulsifying materials are also included in emulsion formulations and contribute to the properties of emulsions. These include fats, oils, waxes, fatty acids, fatty alcohols, fatty esters, humectants, hydrophilic colloids, preservatives and antioxidants (Block, in Pharmaceutical Dosage Forms, Lieberman, Rieger and Banker (Eds.), 1988, Marcel Dekker, Inc., New York, N.Y., volume 1, p. 335; Idson, in Pharmaceutical Dosage Forms, Lieberman, Rieger and Banker (Eds.), 1988, Marcel Dekker, Inc., New York, N.Y., volume 1, p. 199).

Hydrophilic colloids or hydrocolloids include naturally occurring gums and synthetic polymers such as polysaccharides (for example, acacia, agar, alginic acid, carrageenan, guar gum, karaya gum, and tragacanth), cellulose derivatives (for example, carboxymethylcellulose and carboxypropylcellulose), and synthetic polymers (for example, carbomers, cellulose ethers, and carboxyvinyl polymers). These disperse or swell in water to form colloidal solutions that stabilize emulsions by forming strong interfacial films around the dispersed-phase droplets and by increasing the viscosity of the external phase.

Since emulsions often contain a number of ingredients such as carbohydrates, proteins, sterols and phosphatides that may readily support the growth of microbes, these formulations often incorporate preservatives. Commonly used preservatives included in emulsion formulations include methyl paraben, propyl paraben, quaternary ammonium salts, benzalkonium chloride, esters of p-hydroxybenzoic acid, and boric acid. Antioxidants are also commonly added to emulsion formulations to prevent deterioration of the formulation. Antioxidants used may be free radical scavengers such as tocopherols, alkyl gallates, butylated hydroxyanisole, butylated hydroxytoluene, or reducing agents such as ascorbic acid and sodium metabisulfite, and antioxidant synergists such as citric acid, tartaric acid, and lecithin.

The application of emulsion formulations via dermatological, oral and parenteral routes and methods for their manufacture have been reviewed in the literature (Idson, in Pharmaceutical Dosage Forms, Lieberman, Rieger and Banker (Eds.), 1988, Marcel Dekker, Inc., New York, N.Y., volume 1, p. 199). Emulsion formulations for oral delivery have been very widely used because of ease of formulation, as well as efficacy from an absorption and bioavailability standpoint (Rosoff, in Pharmaceutical Dosage Forms, Lieberman, Rieger and Banker (Eds.), 1988, Marcel Dekker, Inc., New York, N.Y., volume 1, p. 245; Idson, in Pharmaceutical Dosage Forms, Lieberman, Rieger and Banker (Eds.), 1988, Marcel Dekker, Inc., New York, N.Y., volume 1, p. 199). Mineral-oil base laxatives, oil-soluble vitamins and high fat nutritive preparations are among the materials that have commonly been administered orally as o/w emulsions.

In one embodiment of the present invention, the compositions of dsRNAs and nucleic acids are formulated as microemulsions. A microemulsion may be defined as a system of water, oil and amphiphile which is a single optically isotropic and thermodynamically stable liquid solution (Rosoff, in Pharmaceutical Dosage Forms, Lieberman, Rieger and Banker (Eds.), 1988, Marcel Dekker, Inc., New York, N.Y., volume 1, p. 245). Typically microemulsions are systems that are prepared by first dispersing an oil in an aqueous surfactant solution and then adding a sufficient amount of a fourth component, generally an intermediate chain-length alcohol to form a transparent system. Therefore, microemulsions have also been described as thermodynamically stable, isotropically clear dispersions of two immiscible liquids that are stabilized by interfacial films of surface-active molecules (Leung and Shah, in: Controlled Release of Drugs: Polymers and Aggregate Systems, Rosoff, M., Ed., 1989, VCH Publishers, New York, pages 185-215). Microemulsions commonly are prepared via a combination of three to five components that include oil, water, surfactant, cosurfactant and electrolyte. Whether the microemulsion is of the water-in-oil (w/o) or an oil-in-water (o/w) type is dependent on the properties of the oil and surfactant used and on the structure and geometric packing of the polar heads and hydrocarbon tails of the surfactant molecules (Schott, in Remington's Pharmaceutical Sciences, Mack Publishing Co., Easton, Pa., 1985, p. 271).

The phenomenological approach utilizing phase diagrams has been extensively studied and has yielded a comprehensive knowledge, to one skilled in the art, of how to formulate microemulsions (Rosoff, in Pharmaceutical Dosage Forms, Lieberman, Rieger and Banker (Eds.), 1988, Marcel Dekker, Inc., New York, N.Y., volume 1, p. 245; Block, in Pharmaceutical Dosage Forms, Lieberman, Rieger and Banker (Eds.), 1988, Marcel Dekker, Inc., New York, N.Y., volume 1, p. 335). Compared to conventional emulsions, microemulsions offer the advantage of solubilizing water-insoluble drugs in a formulation of thermodynamically stable droplets that are formed spontaneously.

Surfactants used in the preparation of microemulsions include, but are not limited to, ionic surfactants, non-ionic surfactants, Brij 96, polyoxyethylene oleyl ethers, polyglycerol fatty acid esters, tetraglycerol monolaurate (ML310), tetraglycerol monooleate (MO310), hexaglycerol monooleate (PO310), hexaglycerol pentaoleate (PO500), decaglycerol monocaprate (MCA750), decaglycerol monooleate (MO750), decaglycerol sequioleate (SO750), decaglycerol decaoleate (DAO750), alone or in combination with cosurfactants. The cosurfactant, usually a short-chain alcohol such as ethanol, 1-propanol, and 1-butanol, serves to increase the interfacial fluidity by penetrating into the surfactant film and consequently creating a disordered film because of the void space generated among surfactant molecules. Microemulsions may, however, be prepared without the use of cosurfactants and alcohol-free self-emulsifying microemulsion systems are known in the art. The aqueous phase may typically be, but is not limited to, water, an aqueous solution of the drug, glycerol, PEG300, PEG400, polyglycerols, propylene glycols, and derivatives of ethylene glycol. The oil phase may include, but is not limited to, materials such as Captex 300, Captex 355, Capmul MCM, fatty acid esters, medium chain (C8-C12) mono, di, and tri-glycerides, polyoxyethylated glyceryl fatty acid esters, fatty alcohols, polyglycolized glycerides, saturated polyglycolized C8-C10 glycerides, vegetable oils and silicone oil.

Microemulsions are particularly of interest from the standpoint of drug solubilization and the enhanced absorption of drugs. Lipid based microemulsions (both o/w and w/o) have been proposed to enhance the oral bioavailability of drugs, including peptides (Constantinides et al., Pharmaceutical Research, 1994, 11, 1385-1390; Ritschel, Meth. Find. Exp. Clin. Pharmacol., 1993, 13, 205). Microemulsions afford advantages of improved drug solubilization, protection of drug from enzymatic hydrolysis, possible enhancement of drug absorption due to surfactant-induced alterations in membrane fluidity and permeability, ease of preparation, ease of oral administration over solid dosage forms, improved clinical potency, and decreased toxicity (Constantinides et al., Pharmaceutical Research, 1994, 11, 1385; Ho et al., J. Pharm. Sci., 1996, 85, 138-143). Often microemulsions may form spontaneously when their components are brought together at ambient temperature. This may be particularly advantageous when formulating thermolabile drugs, peptides or dsRNAs. Microemulsions have also been effective in the transdermal delivery of active components in both cosmetic and pharmaceutical applications. It is expected that the microemulsion compositions and formulations of the present invention will facilitate the increased systemic absorption of dsRNAs and nucleic acids from the gastrointestinal tract, as well as improve the local cellular uptake of dsRNAs and nucleic acids.

Microemulsions of the present invention may also contain additional components and additives such as sorbitan monostearate (Grill 3), Labrasol, and penetration enhancers to improve the properties of the formulation and to enhance the absorption of the dsRNAs and nucleic acids of the present invention. Penetration enhancers used in the microemulsions of the present invention may be classified as belonging to one of five broad categories—surfactants, fatty acids, bile salts, chelating agents, and non-chelating non-surfactants (Lee et al., Critical Reviews in Therapeutic Drug Carrier Systems, 1991, p. 92). Each of these classes has been discussed above.

Penetration Enhancers

In one embodiment, the present invention employs various penetration enhancers to effect the efficient delivery of nucleic acids, particularly dsRNAs, to the skin of animals. Most drugs are present in solution in both ionized and nonionized forms. However, usually only lipid soluble or lipophilic drugs readily cross cell membranes. It has been discovered that even non-lipophilic drugs may cross cell membranes if the membrane to be crossed is treated with a penetration enhancer. In addition to aiding the diffusion of non-lipophilic drugs across cell membranes, penetration enhancers also enhance the permeability of lipophilic drugs.

Penetration enhancers may be classified as belonging to one of five broad categories, i.e., surfactants, fatty acids, bile salts, chelating agents, and non-chelating non-surfactants (Lee et al., Critical Reviews in Therapeutic Drug Carrier Systems, 1991, p. 92). Each of the above mentioned classes of penetration enhancers are described below in greater detail.

Surfactants: In connection with the present invention, surfactants (or “surface-active agents”) are chemical entities which, when dissolved in an aqueous solution, reduce the surface tension of the solution or the interfacial tension between the aqueous solution and another liquid, with the result that absorption of dsRNAs through the mucosa is enhanced. In addition to bile salts and fatty acids, these penetration enhancers include, for example, sodium lauryl sulfate, polyoxyethylene-9-lauryl ether and polyoxyethylene-20-cetyl ether) (Lee et al., Critical Reviews in Therapeutic Drug Carrier Systems, 1991, p. 92); and perfluorochemical emulsions, such as FC-43. Takahashi et al., J. Pharm. Pharmacol., 1988, 40, 252).

Fatty acids: Various fatty acids and their derivatives which act as penetration enhancers include, for example, oleic acid, lauric acid, capric acid (n-decanoic acid), myristic acid, palmitic acid, stearic acid, linoleic acid, linolenic acid, dicaprate, tricaprate, monoolein (1-monooleoyl-rac-glycerol), dilaurin, caprylic acid, arachidonic acid, glycerol 1-monocaprate, 1-dodecylazacycloheptan-2-one, acylcarnitines, acylcholines, C₁₋₁₀ alkyl esters thereof (e.g., methyl, isopropyl and t-butyl), and mono- and di-glycerides thereof (i.e., oleate, laurate, caprate, myristate, palmitate, stearate, linoleate, etc.) (Lee et al., Critical Reviews in Therapeutic Drug Carrier Systems, 1991, p. 92; Muranishi, Critical Reviews in Therapeutic Drug Carrier Systems, 1990, 7, 1-33; El Hariri et al., J. Pharm. Pharmacol., 1992, 44, 651-654).

Bile salts: The physiological role of bile includes the facilitation of dispersion and absorption of lipids and fat-soluble vitamins (Brunton, Chapter 38 in: Goodman & Gilman's The Pharmacological Basis of Therapeutics, 9th Ed., Hardman et al. Eds., McGraw-Hill, New York, 1996, pp. 934-935). Various natural bile salts, and their synthetic derivatives, act as penetration enhancers. Thus the term “bile salts” includes any of the naturally occurring components of bile as well as any of their synthetic derivatives. Suitable bile salts include, for example, cholic acid (or its pharmaceutically acceptable sodium salt, sodium cholate), dehydrocholic acid (sodium dehydrocholate), deoxycholic acid (sodium deoxycholate), glucholic acid (sodium glucholate), glycholic acid (sodium glycocholate), glycodeoxycholic acid (sodium glycodeoxycholate), taurocholic acid (sodium taurocholate), taurodeoxycholic acid (sodium taurodeoxycholate), chenodeoxycholic acid (sodium chenodeoxycholate), ursodeoxycholic acid (UDCA), sodium tauro-24,25-dihydro-fusidate (STDHF), sodium glycodihydrofusidate and polyoxyethylene-9-lauryl ether (POE) (Lee et al., Critical Reviews in Therapeutic Drug Carrier Systems, 1991, page 92; Swinyard, Chapter 39 In: Remington's Pharmaceutical Sciences, 18th Ed., Gennaro, ed., Mack Publishing Co., Easton, Pa., 1990, pages 782-783; Muranishi, Critical Reviews in Therapeutic Drug Carrier Systems, 1990, 7, 1-33; Yamamoto et al., J. Pharm. Exp. Ther., 1992, 263, 25; Yamashita et al., J. Pharm. Sci., 1990, 79, 579-583).

Chelating Agents: Chelating agents, as used in connection with the present invention, can be defined as compounds that remove metallic ions from solution by forming complexes therewith, with the result that absorption of dsRNAs through the mucosa is enhanced. With regards to their use as penetration enhancers in the present invention, chelating agents have the added advantage of also serving as DNase inhibitors, as most characterized DNA nucleases require a divalent metal ion for catalysis and are thus inhibited by chelating agents (Jarrett, J. Chromatogr., 1993, 618, 315-339). Suitable chelating agents include but are not limited to disodium ethylenediaminetetraacetate (EDTA), citric acid, salicylates (e.g., sodium salicylate, 5-methoxysalicylate and homovanilate), N-acyl derivatives of collagen, laureth-9 and N-amino acyl derivatives of beta-diketones (enamines) (Lee et al., Critical Reviews in Therapeutic Drug Carrier Systems, 1991, page 92; Muranishi, Critical Reviews in Therapeutic Drug Carrier Systems, 1990, 7, 1-33; Buur et al., J. Control Rel., 1990, 14, 43-51).

Non-chelating non-surfactants: As used herein, non-chelating non-surfactant penetration enhancing compounds can be defined as compounds that demonstrate insignificant activity as chelating agents or as surfactants but that nonetheless enhance absorption of dsRNAs through the alimentary mucosa (Muranishi, Critical Reviews in Therapeutic Drug Carrier Systems, 1990, 7, 1-33). This class of penetration enhancers include, for example, unsaturated cyclic ureas, 1-alkyl- and 1-alkenylazacyclo-alkanone derivatives (Lee et al., Critical Reviews in Therapeutic Drug Carrier Systems, 1991, page 92); and non-steroidal anti-inflammatory agents such as diclofenac sodium, indomethacin and phenylbutazone (Yamashita et al., J. Pharm. Pharmacol., 1987, 39, 621-626).

Agents that enhance uptake of dsRNAs at the cellular level may also be added to the pharmaceutical and other compositions of the present invention. For example, cationic lipids, such as lipofectin (Junichi et al, U.S. Pat. No. 5,705,188), cationic glycerol derivatives, and polycationic molecules, such as polylysine (Lollo et al., PCT Application WO 97/30731), are also known to enhance the cellular uptake of dsRNAs.

Other agents may be utilized to enhance the penetration of the administered nucleic acids, including glycols such as ethylene glycol and propylene glycol, pyrrols such as 2-pyrrol, azones, and terpenes such as limonene and menthone.

Carriers

The agent and dsRNAs targeting a gene of interest of the present invention can be formulated in a pharmaceutically acceptable carrier or diluent. A “pharmaceutically acceptable carrier” (also referred to herein as an “excipient”) is a pharmaceutically acceptable solvent, suspending agent, or any other pharmacologically inert vehicle. Pharmaceutically acceptable carriers can be liquid or solid, and can be selected with the planned manner of administration in mind so as to provide for the desired bulk, consistency, and other pertinent transport and chemical properties. Typical pharmaceutically acceptable carriers include, by way of example and not limitation: water; saline solution; binding agents (e.g., polyvinylpyrrolidone or hydroxypropyl methylcellulose); fillers (e.g., lactose and other sugars, gelatin, or calcium sulfate); lubricants (e.g., starch, polyethylene glycol, or sodium acetate); disintegrates (e.g., starch or sodium starch glycolate); and wetting agents (e.g., sodium lauryl sulfate).

Certain compositions of the present invention also incorporate carrier compounds in the formulation. As used herein, “carrier compound” or “carrier” can refer to a nucleic acid, or analog thereof, which is inert (i.e., does not possess biological activity per se) but is recognized as a nucleic acid by in vivo processes that reduce the bioavailability of a nucleic acid having biological activity by, for example, degrading the biologically active nucleic acid or promoting its removal from circulation. The co-administration of a nucleic acid and a carrier compound, typically with an excess of the latter substance, can result in a substantial reduction of the amount of nucleic acid recovered in the liver, kidney or other extra-circulatory reservoirs, presumably due to competition between the carrier compound and the nucleic acid for a common receptor. For example, the recovery of a partially phosphorothioate dsRNA in hepatic tissue can be reduced when it is co-administered with polyinosinic acid, dextran sulfate, polycytidic acid or 4-acetamido-4′isothiocyano-stilbene-2,2′-disulfonic acid (Miyao et al., DsRNA Res. Dev., 1995, 5, 115-121; Takakura et al., DsRNA & Nucl. Acid Drug Dev., 1996, 6, 177-183.

Excipients

In contrast to a carrier compound, a “pharmaceutical carrier” or “excipient” is a pharmaceutically acceptable solvent, suspending agent or any other pharmacologically inert vehicle for delivering one or more nucleic acids to an animal. The excipient may be liquid or solid and is selected, with the planned manner of administration in mind, so as to provide for the desired bulk, consistency, etc., when combined with a nucleic acid and the other components of a given pharmaceutical composition. Typical pharmaceutical carriers include, but are not limited to, binding agents (e.g., pregelatinized maize starch, polyvinylpyrrolidone or hydroxypropyl methylcellulose, etc.); fillers (e.g., lactose and other sugars, microcrystalline cellulose, pectin, gelatin, calcium sulfate, ethyl cellulose, polyacrylates or calcium hydrogen phosphate, etc.); lubricants (e.g., magnesium stearate, talc, silica, colloidal silicon dioxide, stearic acid, metallic stearates, hydrogenated vegetable oils, corn starch, polyethylene glycols, sodium benzoate, sodium acetate, etc.); disintegrants (e.g., starch, sodium starch glycolate, etc.); and wetting agents (e.g., sodium lauryl sulphate, etc).

Pharmaceutically acceptable organic or inorganic excipients suitable for non-parenteral administration which do not deleteriously react with nucleic acids can also be used to formulate the compositions of the present invention. Suitable pharmaceutically acceptable carriers include, but are not limited to, water, salt solutions, alcohols, polyethylene glycols, gelatin, lactose, amylose, magnesium stearate, talc, silicic acid, viscous paraffin, hydroxymethylcellulose, polyvinylpyrrolidone and the like.

Formulations for topical administration of nucleic acids may include sterile and non-sterile aqueous solutions, non-aqueous solutions in common solvents such as alcohols, or solutions of the nucleic acids in liquid or solid oil bases. The solutions may also contain buffers, diluents and other suitable additives. Pharmaceutically acceptable organic or inorganic excipients suitable for non-parenteral administration which do not deleteriously react with nucleic acids can be used.

Suitable pharmaceutically acceptable excipients include, but are not limited to, water, salt solutions, alcohol, polyethylene glycols, gelatin, lactose, amylose, magnesium stearate, talc, silicic acid, viscous paraffin, hydroxymethylcellulose, polyvinylpyrrolidone and the like.

Other Components

The compositions of the present invention may additionally contain other adjunct components conventionally found in pharmaceutical compositions, at their art-established usage levels. Thus, for example, the compositions may contain additional, compatible, pharmaceutically-active materials such as, for example, antipruritics, astringents, local anesthetics or anti-inflammatory agents, or may contain additional materials useful in physically formulating various dosage forms of the compositions of the present invention, such as dyes, flavoring agents, preservatives, antioxidants, opacifiers, thickening agents and stabilizers. However, such materials, when added, should not unduly interfere with the biological activities of the components of the compositions of the present invention. The formulations can be sterilized and, if desired, mixed with auxiliary agents, e.g., lubricants, preservatives, stabilizers, wetting agents, emulsifiers, salts for influencing osmotic pressure, buffers, colorings, flavorings and/or aromatic substances and the like which do not deleteriously interact with the nucleic acid(s) of the formulation.

Aqueous suspensions may contain substances which increase the viscosity of the suspension including, for example, sodium carboxymethylcellulose, sorbitol and/or dextran. The suspension may also contain stabilizers.

Methods of Preparing Lipid Particles

The methods and compositions of the invention make use of certain cationic lipids, the synthesis, preparation and characterization of which is described below and in the accompanying Examples. In addition, the present invention provides methods of preparing lipid particles, including those associated with a therapeutic agent, e.g., a nucleic acid. In the methods described herein, a mixture of lipids is combined with a buffered aqueous solution of nucleic acid to produce an intermediate mixture containing nucleic acid encapsulated in lipid particles wherein the encapsulated nucleic acids are present in a nucleic acid/lipid ratio of about 3 wt % to about 25 wt %, preferably 5 to 15 wt %. The intermediate mixture may optionally be sized to obtain lipid-encapsulated nucleic acid particles wherein the lipid portions are unilamellar vesicles, preferably having a diameter of 30 to 150 nm, more preferably about 40 to 90 nm. The pH is then raised to neutralize at least a portion of the surface charges on the lipid-nucleic acid particles, thus providing an at least partially surface-neutralized lipid-encapsulated nucleic acid composition.

As described above, several of these cationic lipids are amino lipids that are charged at a pH below the pK_(a) of the amino group and substantially neutral at a pH above the pK_(a). These cationic lipids are termed titratable cationic lipids and can be used in the formulations of the invention using a two-step process. First, lipid vesicles can be formed at the lower pH with titratable cationic lipids and other vesicle components in the presence of nucleic acids. In this manner, the vesicles will encapsulate and entrap the nucleic acids. Second, the surface charge of the newly formed vesicles can be neutralized by increasing the pH of the medium to a level above the pK_(a) of the titratable cationic lipids present, i.e., to physiological pH or higher. Particularly advantageous aspects of this process include both the facile removal of any surface adsorbed nucleic acid and a resultant nucleic acid delivery vehicle which has a neutral surface. Liposomes or lipid particles having a neutral surface are expected to avoid rapid clearance from circulation and to avoid certain toxicities which are associated with cationic liposome preparations. Additional details concerning these uses of such titratable cationic lipids in the formulation of nucleic acid-lipid particles are provided in U.S. Pat. No. 6,287,591 and U.S. Pat. No. 6,858,225, incorporated herein by reference.

It is further noted that the vesicles formed in this manner provide formulations of uniform vesicle size with high content of nucleic acids. Additionally, the vesicles have a size range of from about 30 to about 150 nm, more preferably about 30 to about 90 nm.

Without intending to be bound by any particular theory, it is believed that the very high efficiency of nucleic acid encapsulation is a result of electrostatic interaction at low pH. At acidic pH (e.g. pH 4.0) the vesicle surface is charged and binds a portion of the nucleic acids through electrostatic interactions. When the external acidic buffer is exchanged for a more neutral buffer (e.g. pH 7.5) the surface of the lipid particle or liposome is neutralized, allowing any external nucleic acid to be removed. More detailed information on the formulation process is provided in various publications (e.g., U.S. Pat. No. 6,287,591 and U.S. Pat. No. 6,858,225).

In view of the above, the present invention provides methods of preparing lipid/nucleic acid formulations. In the methods described herein, a mixture of lipids is combined with a buffered aqueous solution of nucleic acid to produce an intermediate mixture containing nucleic acid encapsulated in lipid particles, e.g., wherein the encapsulated nucleic acids are present in a nucleic acid/lipid ratio of about 10 wt % to about 20 wt %. The intermediate mixture may optionally be sized to obtain lipid-encapsulated nucleic acid particles wherein the lipid portions are unilamellar vesicles, preferably having a diameter of 30 to 150 nm, more preferably about 40 to 90 nm. The pH is then raised to neutralize at least a portion of the surface charges on the lipid-nucleic acid particles, thus providing an at least partially surface-neutralized lipid-encapsulated nucleic acid composition.

In certain embodiments, the mixture of lipids includes at least two lipid components: a first amino lipid component of the present invention that is selected from among lipids which have a pKa such that the lipid is cationic at pH below the pKa and neutral at pH above the pKa, and a second lipid component that is selected from among lipids that prevent particle aggregation during lipid-nucleic acid particle formation. In particular embodiments, the amino lipid is a novel cationic lipid of the present invention.

In preparing the nucleic acid-lipid particles of the invention, the mixture of lipids is typically a solution of lipids in an organic solvent. This mixture of lipids can then be dried to form a thin film or lyophilized to form a powder before being hydrated with an aqueous buffer to form liposomes. Alternatively, in a preferred method, the lipid mixture can be solubilized in a water miscible alcohol, such as ethanol, and this ethanolic solution added to an aqueous buffer resulting in spontaneous liposome formation. In most embodiments, the alcohol is used in the form in which it is commercially available. For example, ethanol can be used as absolute ethanol (100%), or as 95% ethanol, the remainder being water. This method is described in more detail in U.S. Pat. No. 5,976,567).

In accordance with the invention, the lipid mixture is combined with a buffered aqueous solution that may contain the nucleic acids. The buffered aqueous solution of is typically a solution in which the buffer has a pH of less than the pK_(a) of the protonatable lipid in the lipid mixture. Examples of suitable buffers include citrate, phosphate, acetate, and MES. A particularly preferred buffer is citrate buffer. Preferred buffers will be in the range of 1-1000 mM of the anion, depending on the chemistry of the nucleic acid being encapsulated, and optimization of buffer concentration may be significant to achieving high loading levels (see, e.g., U.S. Pat. No. 6,287,591 and U.S. Pat. No. 6,858,225). Alternatively, pure water acidified to pH 5-6 with chloride, sulfate or the like may be useful. In this case, it may be suitable to add 5% glucose, or another non-ionic solute which will balance the osmotic potential across the particle membrane when the particles are dialyzed to remove ethanol, increase the pH, or mixed with a pharmaceutically acceptable carrier such as normal saline. The amount of nucleic acid in buffer can vary, but will typically be from about 0.01 mg/mL to about 200 mg/mL, more preferably from about 0.5 mg/mL to about 50 mg/mL.

The mixture of lipids and the buffered aqueous solution of therapeutic nucleic acids is combined to provide an intermediate mixture. The intermediate mixture is typically a mixture of lipid particles having encapsulated nucleic acids. Additionally, the intermediate mixture may also contain some portion of nucleic acids which are attached to the surface of the lipid particles (liposomes or lipid vesicles) due to the ionic attraction of the negatively-charged nucleic acids and positively-charged lipids on the lipid particle surface (the amino lipids or other lipid making up the protonatable first lipid component are positively charged in a buffer having a pH of less than the pK_(a) of the protonatable group on the lipid). In one group of preferred embodiments, the mixture of lipids is an alcohol solution of lipids and the volumes of each of the solutions is adjusted so that upon combination, the resulting alcohol content is from about 20% by volume to about 45% by volume. The method of combining the mixtures can include any of a variety of processes, often depending upon the scale of formulation produced. For example, when the total volume is about 10-20 mL or less, the solutions can be combined in a test tube and stirred together using a vortex mixer. Large-scale processes can be carried out in suitable production scale glassware.

Optionally, the lipid-encapsulated therapeutic agent (e.g., nucleic acid) complexes which are produced by combining the lipid mixture and the buffered aqueous solution of therapeutic agents (nucleic acids) can be sized to achieve a desired size range and relatively narrow distribution of lipid particle sizes. Preferably, the compositions provided herein will be sized to a mean diameter of from about 70 to about 200 nm, more preferably about 90 to about 130 nm. Several techniques are available for sizing liposomes to a desired size. One sizing method is described in U.S. Pat. No. 4,737,323, incorporated herein by reference. Sonicating a liposome suspension either by bath or probe sonication produces a progressive size reduction down to small unilamellar vesicles (SUVs) less than about 0.05 microns in size. Homogenization is another method which relies on shearing energy to fragment large liposomes into smaller ones. In a typical homogenization procedure, multilamellar vesicles are recirculated through a standard emulsion homogenizer until selected liposome sizes, typically between about 0.1 and 0.5 microns, are observed. In both methods, the particle size distribution can be monitored by conventional laser-beam particle size determination. For certain methods herein, extrusion is used to obtain a uniform vesicle size.

Extrusion of liposome compositions through a small-pore polycarbonate membrane or an asymmetric ceramic membrane results in a relatively well-defined size distribution. Typically, the suspension is cycled through the membrane one or more times until the desired liposome complex size distribution is achieved. The liposomes may be extruded through successively smaller-pore membranes, to achieve a gradual reduction in liposome size. In some instances, the lipid-nucleic acid compositions which are formed can be used without any sizing.

In particular embodiments, methods of the present invention further comprise a step of neutralizing at least some of the surface charges on the lipid portions of the lipid-nucleic acid compositions. By at least partially neutralizing the surface charges, unencapsulated nucleic acid is freed from the lipid particle surface and can be removed from the composition using conventional techniques. Preferably, unencapsulated and surface adsorbed nucleic acids are removed from the resulting compositions through exchange of buffer solutions. For example, replacement of a citrate buffer (pH about 4.0, used for forming the compositions) with a HEPES-buffered saline (HBS pH about 7.5) solution, results in the neutralization of liposome surface and nucleic acid release from the surface. The released nucleic acid can then be removed via chromatography using standard methods, and then switched into a buffer with a pH above the pKa of the lipid used.

Optionally the lipid vesicles (i.e., lipid particles) can be formed by hydration in an aqueous buffer and sized using any of the methods described above prior to addition of the nucleic acid. As described above, the aqueous buffer should be of a pH below the pKa of the amino lipid. A solution of the nucleic acids can then be added to these sized, preformed vesicles. To allow encapsulation of nucleic acids into such “pre-formed” vesicles the mixture should contain an alcohol, such as ethanol. In the case of ethanol, it should be present at a concentration of about 20% (w/w) to about 45% (w/w). In addition, it may be necessary to warm the mixture of pre-formed vesicles and nucleic acid in the aqueous buffer-ethanol mixture to a temperature of about 25° C. to about 50° C. depending on the composition of the lipid vesicles and the nature of the nucleic acid. It will be apparent to one of ordinary skill in the art that optimization of the encapsulation process to achieve a desired level of nucleic acid in the lipid vesicles will require manipulation of variable such as ethanol concentration and temperature. Examples of suitable conditions for nucleic acid encapsulation are provided in the Examples. Once the nucleic acids are encapsulated within the preformed vesicles, the external pH can be increased to at least partially neutralize the surface charge. Unencapsulated and surface adsorbed nucleic acids can then be removed as described above.

Methods of Use

The lipid particles of the invention may be used to deliver a therapeutic agent to a cell, in vitro or in vivo. In particular embodiments, the therapeutic agent is a nucleic acid, which is delivered to a cell using a nucleic acid-lipid particles of the invention. While the following description of various methods of using the lipid particles and related pharmaceutical compositions of the invention are exemplified by description related to nucleic acid-lipid particles, it is understood that these methods and compositions may be readily adapted for the delivery of any therapeutic agent for the treatment of any disease or disorder that would benefit from such treatment.

In certain embodiments, the invention provides methods for introducing a nucleic acid into a cell. Preferred nucleic acids for introduction into cells are siRNA, immune-stimulating oligonucleotides, plasmids, antisense and ribozymes. These methods may be carried out by contacting the particles or compositions of the invention with the cells for a period of time sufficient for intracellular delivery to occur.

The compositions of the invention can be adsorbed to almost any cell type. Once adsorbed, the nucleic acid-lipid particles can either be endocytosed by a portion of the cells, exchange lipids with cell membranes, or fuse with the cells. Transfer or incorporation of the nucleic acid portion of the complex can take place via any one of these pathways. Without intending to be limited with respect to the scope of the invention, it is believed that in the case of particles taken up into the cell by endocytosis the particles then interact with the endosomal membrane, resulting in destabilization of the endosomal membrane, possibly by the formation of non-bilayer phases, resulting in introduction of the encapsulated nucleic acid into the cell cytoplasm. Similarly in the case of direct fusion of the particles with the cell plasma membrane, when fusion takes place, the liposome membrane is integrated into the cell membrane and the contents of the liposome combine with the intracellular fluid. Contact between the cells and the lipid-nucleic acid compositions, when carried out in vitro, will take place in a biologically compatible medium. The concentration of compositions can vary widely depending on the particular application, but is generally between about 1 μmol and about 10 mmol. In certain embodiments, treatment of the cells with the lipid-nucleic acid compositions will generally be carried out at physiological temperatures (about 37° C.) for periods of time from about 1 to 24 hours, preferably from about 2 to 8 hours. For in vitro applications, the delivery of nucleic acids can be to any cell grown in culture, whether of plant or animal origin, vertebrate or invertebrate, and of any tissue or type. In preferred embodiments, the cells will be animal cells, more preferably mammalian cells, and most preferably human cells.

In one group of embodiments, a lipid-nucleic acid particle suspension is added to 60-80% confluent plated cells having a cell density of from about 10³ to about 10⁵ cells/mL, more preferably about 2×10⁴ cells/mL. The concentration of the suspension added to the cells is preferably of from about 0.01 to 20 μg/mL, more preferably about 1 μg/mL.

Typical applications include using well known procedures to provide intracellular delivery of siRNA to knock down or silence specific cellular targets. Alternatively applications include delivery of DNA or mRNA sequences that code for therapeutically useful polypeptides. In this manner, therapy is provided for genetic diseases by supplying deficient or absent gene products (i.e., for Duchenne's dystrophy, see Kunkel, et al., Brit. Med. Bull. 45(3):630-643 (1989), and for cystic fibrosis, see Goodfellow, Nature 341:102-103 (1989)). Other uses for the compositions of the invention include introduction of antisense oligonucleotides in cells (see, Bennett, et al., Mol. Pharm. 41:1023-1033 (1992)).

Alternatively, the compositions of the invention can also be used for deliver of nucleic acids to cells in vivo, using methods which are known to those of skill in the art. With respect to application of the invention for delivery of DNA or mRNA sequences, Zhu, et al., Science 261:209-211 (1993), incorporated herein by reference, describes the intravenous delivery of cytomegalovirus (CMV)-chloramphenicol acetyltransferase (CAT) expression plasmid using DOTMA-DOPE complexes. Hyde, et al., Nature 362:250-256 (1993), incorporated herein by reference, describes the delivery of the cystic fibrosis transmembrane conductance regulator (CFTR) gene to epithelia of the airway and to alveoli in the lung of mice, using liposomes. Brigham, et al., Am. J. Med. Sci. 298:278-281 (1989), incorporated herein by reference, describes the in vivo transfection of lungs of mice with a functioning prokaryotic gene encoding the intracellular enzyme, chloramphenicol acetyltransferase (CAT). Thus, the compositions of the invention can be used in the treatment of infectious diseases.

For in vivo administration, the pharmaceutical compositions are preferably administered parenterally, i.e., intraarticularly, intravenously, intraperitoneally, subcutaneously, or intramuscularly. In particular embodiments, the pharmaceutical compositions are administered intravenously or intraperitoneally by a bolus injection. For one example, see Stadler, et al., U.S. Pat. No. 5,286,634, which is incorporated herein by reference. Intracellular nucleic acid delivery has also been discussed in Straubringer, et al., METHODS IN ENZYMOLOGY, Academic Press, New York. 101:512-527 (1983); Mannino, et al., Biotechniques 6:682-690 (1988); Nicolau, et al., Crit. Rev. Ther. Drug Carrier Syst. 6:239-271 (1989), and Behr, Acc. Chem. Res. 26:274-278 (1993). Still other methods of administering lipid-based therapeutics are described in, for example, Rahman et al., U.S. Pat. No. 3,993,754; Sears, U.S. Pat. No. 4,145,410; Papahadjopoulos et al., U.S. Pat. No. 4,235,871; Schneider, U.S. Pat. No. 4,224,179; Lenk et al., U.S. Pat. No. 4,522,803; and Fountain et al., U.S. Pat. No. 4,588,578.

In other methods, the pharmaceutical preparations may be contacted with the target tissue by direct application of the preparation to the tissue. The application may be made by topical, “open” or “closed” procedures. By “topical,” it is meant the direct application of the pharmaceutical preparation to a tissue exposed to the environment, such as the skin, oropharynx, external auditory canal, and the like. “Open” procedures are those procedures which include incising the skin of a patient and directly visualizing the underlying tissue to which the pharmaceutical preparations are applied. This is generally accomplished by a surgical procedure, such as a thoracotomy to access the lungs, abdominal laparotomy to access abdominal viscera, or other direct surgical approach to the target tissue. “Closed” procedures are invasive procedures in which the internal target tissues are not directly visualized, but accessed via inserting instruments through small wounds in the skin. For example, the preparations may be administered to the peritoneum by needle lavage. Likewise, the pharmaceutical preparations may be administered to the meninges or spinal cord by infusion during a lumbar puncture followed by appropriate positioning of the patient as commonly practiced for spinal anesthesia or metrazamide imaging of the spinal cord. Alternatively, the preparations may be administered through endoscopic devices.

The lipid-nucleic acid compositions can also be administered in an aerosol inhaled into the lungs (see, Brigham, et al., Am. J. Sci. 298(4):278-281 (1989)) or by direct injection at the site of disease (Culver, Human Gene Therapy, MaryAnn Liebert, Inc., Publishers, New York. pp. 70-71 (1994)).

The methods of the invention may be practiced in a variety of hosts. Preferred hosts include mammalian species, such as humans, non-human primates, dogs, cats, cattle, horses, sheep, and the like.

Dosages for the lipid-therapeutic agent particles of the invention will depend on the ratio of therapeutic agent to lipid and the administrating physician's opinion based on age, weight, and condition of the patient.

In one embodiment, the invention provides a method of modulating the expression of a target polynucleotide or polypeptide. These methods generally comprise contacting a cell with a lipid particle of the invention that is associated with a nucleic acid capable of modulating the expression of a target polynucleotide or polypeptide. As used herein, the term “modulating” refers to altering the expression of a target polynucleotide or polypeptide. In different embodiments, modulating can mean increasing or enhancing, or it can mean decreasing or reducing. Methods of measuring the level of expression of a target polynucleotide or polypeptide are known and available in the arts and include, e.g., methods employing reverse transcription-polymerase chain reaction (RT-PCR) and immunohistochemical techniques. In particular embodiments, the level of expression of a target polynucleotide or polypeptide is increased or reduced by at least 10%, 20%, 30%, 40%, 50%, or greater than 50% as compared to an appropriate control value. For example, if increased expression of a polypeptide desired, the nucleic acid may be an expression vector that includes a polynucleotide that encodes the desired polypeptide. On the other hand, if reduced expression of a polynucleotide or polypeptide is desired, then the nucleic acid may be, e.g., an antisense oligonucleotide, siRNA, or microRNA that comprises a polynucleotide sequence that specifically hybridizes to a polynucleotide that encodes the target polypeptide, thereby disrupting expression of the target polynucleotide or polypeptide. Alternatively, the nucleic acid may be a plasmid that expresses such an antisense oligonucleotide, siRNA, or microRNA.

In one particular embodiment, the invention provides a method of modulating the expression of a polypeptide by a cell, comprising providing to a cell a lipid particle that consists of or consists essentially of a cationic lipid of formula A, a neutral lipid, a sterol, a PEG of PEG-modified lipid, e.g., in a molar ratio of about 35-65% of cationic lipid of formula A, 3-12% of the neutral lipid, 15-45% of the sterol, and 0.5-10% of the PEG or PEG-modified lipid, wherein the lipid particle is associated with a nucleic acid capable of modulating the expression of the polypeptide. In particular embodiments, the molar lipid ratio is approximately 60/7.5/31/1.5 or 57.5/7.5/31.5/3.5 (mol % LIPID A/DSPC/Chol/PEG-DMG). In another group of embodiments, the neutral lipid in these compositions is replaced with DPPC (dipalmitoylphosphatidylcholine), POPC, DOPE or SM.

In particular embodiments, the therapeutic agent is selected from an siRNA, a microRNA, an antisense oligonucleotide, and a plasmid capable of expressing an siRNA, a microRNA, or an antisense oligonucleotide, and wherein the siRNA, microRNA, or antisense RNA comprises a polynucleotide that specifically binds to a polynucleotide that encodes the polypeptide, or a complement thereof, such that the expression of the polypeptide is reduced.

In other embodiments, the nucleic acid is a plasmid that encodes the polypeptide or a functional variant or fragment thereof, such that expression of the polypeptide or the functional variant or fragment thereof is increased.

In related embodiments, the invention provides a method of treating a disease or disorder characterized by overexpression of a polypeptide in a subject, comprising providing to the subject a pharmaceutical composition of the invention, wherein the therapeutic agent is selected from an siRNA, a microRNA, an antisense oligonucleotide, and a plasmid capable of expressing an siRNA, a microRNA, or an antisense oligonucleotide, and wherein the siRNA, microRNA, or antisense RNA comprises a polynucleotide that specifically binds to a polynucleotide that encodes the polypeptide, or a complement thereof.

In one embodiment, the pharmaceutical composition comprises a lipid particle that consists of or consists essentially of Lipid A, DSPC, Chol and PEG-DMG, PEG-C-DOMG or PEG-DMA, e.g., in a molar ratio of about 35-65% of cationic lipid of formula A, 3-12% of the neutral lipid, 15-45% of the sterol, and 0.5-10% of the PEG or PEG-modified lipid PEG-DMG, PEG-C-DOMG or PEG-DMA, wherein the lipid particle is associated with the therapeutic nucleic acid. In particular embodiments, the molar lipid ratio is approximately 60/7.5/31/1.5 or 57.5/7.5/31.5/3.5 (mol % LIPID A/DSPC/Chol/PEG-DMG). In another group of embodiments, the neutral lipid in these compositions is replaced with DPPC, POPC, DOPE or SM.

In another related embodiment, the invention includes a method of treating a disease or disorder characterized by underexpression of a polypeptide in a subject, comprising providing to the subject a pharmaceutical composition of the invention, wherein the therapeutic agent is a plasmid that encodes the polypeptide or a functional variant or fragment thereof.

Unless otherwise defined, all technical and scientific terms used herein have the same meaning as commonly understood by one of ordinary skill in the art to which this invention belongs. Although methods and materials similar or equivalent to those described herein can be used in the practice or testing of the invention, suitable methods and materials are described below. All publications, patent applications, patents, and other references mentioned herein are incorporated by reference in their entirety. In case of conflict, the present specification, including definitions, will control. In addition, the materials, methods, and examples are illustrative only and not intended to be limiting.

Methods for Treating Diseases Caused by Infection with the Ebola Virus

The invention relates in particular to the use of a dsRNA or a pharmaceutical composition prepared therefrom for the treatment or prevention of pathological conditions associated with Ebola infection, e.g., systemic hemorrhage and multi-organ failure.

The invention furthermore relates to the use of an dsRNA or a pharmaceutical composition thereof for treating systemic hemorrhage and multi-organ failure in combination with other pharmaceuticals and/or other therapeutic methods, e.g., with known pharmaceuticals and/or known therapeutic methods, such as, for example, those which are currently employed for treating viral infection and systemic hemorrhage. Preference is given to a combination with interferon or other antiviral agents.

Methods for Inhibiting Expression of a Gene from the Ebola Virus

In yet another aspect, the invention provides a method for inhibiting the expression of a gene from the Ebola virus in a mammal. The method comprises administering a composition of the invention to the mammal such that expression of the target Ebola genome is silenced. Because of their high specificity, the dsRNAs of the invention specifically target RNAs (primary or processed) of the target Ebola gene. Compositions and methods for inhibiting the expression of these Ebola genes using dsRNAs can be performed as described elsewhere herein.

In one embodiment, the method comprises administering a composition comprising a dsRNA, wherein the dsRNA comprises a nucleotide sequence which is complementary to at least a part of an RNA transcript of a gene from the Ebola virus, to the mammal to be treated. When the organism to be treated is a mammal such as a human, the composition may be administered by any means known in the art including, but not limited to oral or parenteral routes, including intravenous, intraperitoneal, intramuscular, subcutaneous, transdermal, airway (aerosol), nasal, administration. In some embodiments, the compositions are administered by intravenous infusion or injection.

Unless otherwise defined, all technical and scientific terms used herein have the same meaning as commonly understood by one of ordinary skill in the art to which this invention belongs.

EXAMPLES Example 1 dsRNA Synthesis

Source of Reagents

Where the source of a reagent is not specifically given herein, such reagent may be obtained from any supplier of reagents for molecular biology at a quality/purity standard for application in molecular biology.

siRNA Synthesis

Single-stranded RNAs were produced by solid phase synthesis on a scale of 1 μmole using an Expedite 8909 synthesizer (Applied Biosystems, Applera Deutschland GmbH, Darmstadt, Germany) and controlled pore glass (CPG, 500 Å, Proligo Biochemie GmbH, Hamburg, Germany) as solid support. RNA and RNA containing 2′-O-methyl nucleotides were generated by solid phase synthesis employing the corresponding phosphoramidites and 2′-O-methyl phosphoramidites, respectively (Proligo Biochemie GmbH, Hamburg, Germany). These building blocks were incorporated at selected sites within the sequence of the oligoribonucleotide chain using standard nucleoside phosphoramidite chemistry such as described in Current protocols in nucleic acid chemistry, Beaucage, S. L. et al. (Edrs.), John Wiley & Sons, Inc., New York, N.Y., USA. Phosphorothioate linkages were introduced by replacement of the iodine oxidizer solution with a solution of the Beaucage reagent (Chruachem Ltd, Glasgow, UK) in acetonitrile (1%). Further ancillary reagents were obtained from Mallinckrodt Baker (Griesheim, Germany).

Deprotection and purification of the crude oligoribonucleotides by anion exchange HPLC were carried out according to established procedures. Yields and concentrations were determined by UV absorption of a solution of the respective RNA at a wavelength of 260 nm using a spectral photometer (DU 640B, Beckman Coulter GmbH, Unterschleilβheim, Germany). Double stranded RNA was generated by mixing an equimolar solution of complementary strands in annealing buffer (20 mM sodium phosphate, pH 6.8; 100 mM sodium chloride), heated in a water bath at 85-90° C. for 3 minutes and cooled to room temperature over a period of 3-4 hours. The annealed RNA solution was stored at −20° C. until use.

For the synthesis of 3′-cholesterol-conjugated siRNAs (herein referred to as -Chol-3), an appropriately modified solid support was used for RNA synthesis. The modified solid support was prepared as follows:

Diethyl-2-azabutane-1,4-dicarboxylate AA

A 4.7 M aqueous solution of sodium hydroxide (50 mL) was added into a stirred, ice-cooled solution of ethyl glycinate hydrochloride (32.19 g, 0.23 mole) in water (50 mL). Then, ethyl acrylate (23.1 g, 0.23 mole) was added and the mixture was stirred at room temperature until completion of the reaction was ascertained by TLC. After 19 h the solution was partitioned with dichloromethane (3×100 mL). The organic layer was dried with anhydrous sodium sulfate, filtered and evaporated. The residue was distilled to afford AA (28.8 g, 61%).

3-{Ethoxycarbonylmethyl-[6-(9H-fluoren-9-ylmethoxycarbonyl-amino)-hexanoyl]-amino}-propionic acid ethyl ester AB

Fmoc-6-amino-hexanoic acid (9.12 g, 25.83 mmol) was dissolved in dichloromethane (50 mL) and cooled with ice. Diisopropylcarbodiimide (3.25 g, 3.99 mL, 25.83 mmol) was added to the solution at 0° C. It was then followed by the addition of Diethyl-azabutane-1,4-dicarboxylate (5 g, 24.6 mmol) and dimethylamino pyridine (0.305 g, 2.5 mmol). The solution was brought to room temperature and stirred further for 6 h. Completion of the reaction was ascertained by TLC. The reaction mixture was concentrated under vacuum and ethyl acetate was added to precipitate diisopropyl urea. The suspension was filtered. The filtrate was washed with 5% aqueous hydrochloric acid, 5% sodium bicarbonate and water. The combined organic layer was dried over sodium sulfate and concentrated to give the crude product which was purified by column chromatography (50% EtOAC/Hexanes) to yield 11.87 g (88%) of AB.

3-[(6-Amino-hexanoyl)-ethoxycarbonylmethyl-amino]-propionic acid ethyl ester AC

3-{Ethoxycarbonylmethyl-[6-(9H-fluoren-9-ylmethoxycarbonylamino)-hexanoyl]-amino}-propionic acid ethyl ester AB (11.5 g, 21.3 mmol) was dissolved in 20% piperidine in dimethylformamide at 0° C. The solution was continued stirring for 1 h. The reaction mixture was concentrated under vacuum, water was added to the residue, and the product was extracted with ethyl acetate. The crude product was purified by conversion into its hydrochloride salt.

3-({6-[17-(1,5-Dimethyl-hexyl)-10,13-dimethyl-2,3,4,7,8,9,10,11,12,13,14,15,16,17-tetradecahydro-1H-cyclopenta[a]phenanthren-3-yloxycarbonylamino]-hexanoyl}ethoxycarbonylmethyl-amino)-propionic acid ethyl ester AD

The hydrochloride salt of 3-[(6-Amino-hexanoyl)-ethoxycarbonylmethyl-amino]-propionic acid ethyl ester AC (4.7 g, 14.8 mmol) was taken up in dichloromethane. The suspension was cooled to 0° C. on ice. To the suspension diisopropylethylamine (3.87 g, 5.2 mL, 30 mmol) was added. To the resulting solution cholesteryl chloroformate (6.675 g, 14.8 mmol) was added. The reaction mixture was stirred overnight. The reaction mixture was diluted with dichloromethane and washed with 10% hydrochloric acid. The product was purified by flash chromatography (10.3 g, 92%).

1-{6-[17-(1,5-Dimethyl-hexyl)-10,13-dimethyl-2,3,4,7,8,9,10,11,12,13,14,15,16,17-tetradecahydro-1H-cyclopenta[a]phenanthren-3-yloxycarbonylamino]-hexanoyl}-4-oxo-pyrrolidine-3-carboxylic acid ethyl ester AE

Potassium t-butoxide (1.1 g, 9.8 mmol) was slurried in 30 mL of dry toluene. The mixture was cooled to 0° C. on ice and 5 g (6.6 mmol) of diester AD was added slowly with stirring within 20 mins. The temperature was kept below 5° C. during the addition. The stirring was continued for 30 mins at 0° C. and 1 mL of glacial acetic acid was added, immediately followed by 4 g of NaH₂PO₄.H₂O in 40 mL of water The resultant mixture was extracted twice with 100 mL of dichloromethane each and the combined organic extracts were washed twice with 10 mL of phosphate buffer each, dried, and evaporated to dryness. The residue was dissolved in 60 mL of toluene, cooled to 0° C. and extracted with three 50 mL portions of cold pH 9.5 carbonate buffer. The aqueous extracts were adjusted to pH 3 with phosphoric acid, and extracted with five 40 mL portions of chloroform which were combined, dried and evaporated to dryness. The residue was purified by column chromatography using 25% ethylacetate/hexane to afford 1.9 g of b-ketoester (39%).

[6-(3-Hydroxy-4-hydroxymethyl-pyrrolidin-1-yl)-6-oxo-hexyl]-carbamic acid 17-(1,5-dimethyl-hexyl)-10,13-dimethyl-2,3,4,7,8,9,10,11,12,13,14,15,16,17-tetradecahydro-1H-cyclopenta[a]phenanthren-3-yl ester AF

Methanol (2 mL) was added dropwise over a period of 1 h to a refluxing mixture of b-ketoester AE (1.5 g, 2.2 mmol) and sodium borohydride (0.226 g, 6 mmol) in tetrahydrofuran (10 mL). Stirring was continued at reflux temperature for 1 h. After cooling to room temperature, 1 N HCl (12.5 mL) was added, the mixture was extracted with ethylacetate (3×40 mL). The combined ethylacetate layer was dried over anhydrous sodium sulfate and concentrated under vacuum to yield the product which was purified by column chromatography (10% MeOH/CHCl₃) (89%).

(6-{3-[Bis-(4-methoxy-phenyl)-phenyl-methoxymethyl]-4-hydroxy-pyrrolidin-1-yl}-6-oxo-hexyl)-carbamic acid 17-(1,5-dimethyl-hexyl)-10,13-dimethyl-2,3,4,7,8,9,10,11,12,14,15,16,17-tetradecahydro-1H-cyclopenta[a]phenanthren-3-yl ester AG

Diol AF (1.25 gm 1.994 mmol) was dried by evaporating with pyridine (2×5 mL) in vacuo. Anhydrous pyridine (10 mL) and 4,4′-dimethoxytritylchloride (0.724 g, 2.13 mmol) were added with stirring. The reaction was carried out at room temperature overnight. The reaction was quenched by the addition of methanol. The reaction mixture was concentrated under vacuum and to the residue dichloromethane (50 mL) was added. The organic layer was washed with 1M aqueous sodium bicarbonate. The organic layer was dried over anhydrous sodium sulfate, filtered and concentrated. The residual pyridine was removed by evaporating with toluene. The crude product was purified by column chromatography (2% MeOH/Chloroform, Rf=0.5 in 5% MeOH/CHCl₃) (1.75 g, 95%).

Succinic acid mono-(4-[bis-(4-methoxy-phenyl)-phenyl-methoxymethyl]-1-{6-[17-(1,5-dimethyl-hexyl)-10,13-dimethyl 2,3,4,7,8,9,10,11,12,13,14,15,16,17-tetradecahydro-1H cyclopenta[a]phenanthren-3-yloxycarbonylamino]-hexanoyl}-pyrrolidin-3-yl) ester AH

Compound AG (1.0 g, 1.05 mmol) was mixed with succinic anhydride (0.150 g, 1.5 mmol) and DMAP (0.073 g, 0.6 mmol) and dried in a vacuum at 40° C. overnight. The mixture was dissolved in anhydrous dichloroethane (3 mL), triethylamine (0.318 g, 0.440 mL, 3.15 mmol) was added and the solution was stirred at room temperature under argon atmosphere for 16 h. It was then diluted with dichloromethane (40 mL) and washed with ice cold aqueous citric acid (5 wt %, 30 mL) and water (2×20 mL). The organic phase was dried over anhydrous sodium sulfate and concentrated to dryness. The residue was used as such for the next step.

Cholesterol Derivatised CPG AI

Succinate AH (0.254 g, 0.242 mmol) was dissolved in a mixture of dichloromethane/acetonitrile (3:2, 3 mL). To that solution DMAP (0.0296 g, 0.242 mmol) in acetonitrile (1.25 mL), 2,2′-Dithio-bis(5-nitropyridine) (0.075 g, 0.242 mmol) in acetonitrile/dichloroethane (3:1, 1.25 mL) were added successively. To the resulting solution triphenylphosphine (0.064 g, 0.242 mmol) in acetonitrile (0.6 ml) was added. The reaction mixture turned bright orange in color. The solution was agitated briefly using a wrist-action shaker (5 mins). Long chain alkyl amine-CPG (LCAA-CPG) (1.5 g, 61 mM) was added. The suspension was agitated for 2 h. The CPG was filtered through a sintered funnel and washed with acetonitrile, dichloromethane and ether successively. Unreacted amino groups were masked using acetic anhydride/pyridine. The achieved loading of the CPG was measured by taking UV measurement (37 mM/g).

The synthesis of siRNAs bearing a 5′-12-dodecanoic acid bisdecylamide group (herein referred to as “5′-C32-”) or a 5′-cholesteryl derivative group (herein referred to as “5′-Chol-”) was performed as described in WO 2004/065601, except that, for the cholesteryl derivative, the oxidation step was performed using the Beaucage reagent in order to introduce a phosphorothioate linkage at the 5′-end of the nucleic acid oligomer.

Nucleic acid sequences are represented below using standard nomenclature, and specifically the abbreviations of Table 1.

TABLE 1 Abbreviations of nucleotide monomers used in nucleic acid sequence representation. It will be understood that these monomers, when present in an oligonucleotide, are mutually linked by 5′-3′-phosphodiester bonds. Abbreviation Nucleotide(s) A adenosine-5′-phosphate C cytidine-5′-phosphate G guanosine-5′-phosphate T, dT 2′-deoxy-thymidine-5′-phosphate U uridine-5′-phosphate N any nucleotide (G, A, C, or T) a 2′-O-methyladenosine-5′-phosphate c 2′-O-methylcytidine-5′-phosphate g 2′-O-methylguanosine-5′-phosphate u 2′-O-methyluridine-5′-phosphate sT, sdT 2′-deoxy-thymidine-5′phosphate-phosphorothioate

Example 2 Gene Walking of a Gene from the Ebola Virus

Design and in Silico Selection of siRNAs Targeting Ebola Virus

siRNA design was carried out to identify siRNAs targeting Ebola virus mRNAs for genes VP30, VP35, NP, L, VP24, VP40 and GP with a focus on sequences isolated from the Zaire region (EBOV-Z), as well as sequences from Sudan (EBOV-S). The siRNA in silico selection resulted in 521 siRNAs satisfying our selection criteria (Table 2).

Ebola Zaire sequence AY354458 was downloaded from NCBI Nucleotide database and further on used as reference sequence for EBOV-Z. Ebola Sudan sequence AY729654 was used as reference sequence for EBOV-S, respectively.

Sequence regions encoding target genes VP30, VP35, NP, L, VP24, VP40 and GP according to the information in the Genbank file were extracted from both reference sequences, followed by extraction of all possible 19mers for each gene, resulting in the candidate siRNA target regions (and siRNA sense sequences) for each distinct gene.

In order to identify siRNAs targeting all available EBOV-Z and EBOV-S sequences, it was necessary to compile available Ebola sequences from all sequenced isolates. For this, each of the 7 target gene sequences extracted from the Ebola Zaire reference sequences was used in a blast search against viruses at NCBI with default parameters and resulting Ebola mRNA hits were downloaded.

Each candidate target region was tested for conservation across the Ebola sequences by searching the relevant target gene for presence of the 19mer target region. The percentage of conserved sequences across all downloaded sequences for the relevant gene was calculated for each candidate target region by dividing of the number of conserved sequences with the total number of downloaded sequences.

Example 3 Ebola siRNA In Vitro Screening

Table 3 provides a summary of the screening results of the siRNAs described in Table 2. Following initial screening using a GFP-expressing Ebola-Zaire virus and immunofluorescence screening using Ebola-Sudan virus, siRNA showing activity were further tested by plaque assay for anti-viral activity against Ebola-Zaire and Ebola-Sudan strains. Several siRNAs were identified that had significant activity against one or more Ebola strains. At a concentration of 100 nM many of the siRNA identified showed greater than a 1 log reduction (>90% inhibition) in Ebola virus titers. Negative control luciferase and GFP siRNA at the same concentration showed reductions in virus titer of between 10 and 35% (Table 3). Three previously identified Ebola siRNA (LS L#1, LS NP#1, LS VP35#1) were also tested in parallel and these inhibited Ebola virus by roughly 70%. The previously identified Ebola siRNA are 25 nucleotide blunt-ended duplexes with the following composition: LS L#1, sense: 5′ CCAUCUCUGAGACACGACAUAUCUU 3′ anti-sense: 5′ AAGAUAUGUCGUGUCUCAGAGAUGG 3′; LS NP#1, sense: 5′ GGUUCAAAGGCAAAUUCAAGUACAU 3′ anti-sense 5′ AUGUACUUGAAUUUGCCUUUGAACC 3′; LS VP35#1, sense 5′ CCCAAAUGCAACAAACCAAGCCAAA 3′ anti-sense 5′ UUUGGCUUGGUUUGUUGCAUUUGGG 3′. The siRNA sequences for AD-1955 and AD-5179 are as follows: AD-1955, sense: 5′ CUUACGCUGAGUACUUCGAdTsdT 3′ anti-sense: 5′ UCGAAGUACUCAGCGUAAGdTsdT 3′; AD-5179, sense: 5′ CcAcAuGAAGcAGcACGACusU 3′ anti-sense: 5′ AAGUCGUGCUGCUUCAUGUGgsusC 3′.

Lead siRNAs were also screened for immunostimulatory activity (IFNalpha and TNFalpha). Immunostimulatory activity was assayed by transfecting siRNAs into human peripheral blood mononuclear cells and measuring cytokine release by ELISA as outlined in Hornung et al. Nature Medicine 2005. Cytokine levels were normalized to a positive control siRNA included in every assay. The lead candidates had no immunostimulatory activity.

The following procedures were used in generating the screening results.

GFP Ebola-Zaire Assay

VERO cells were transfected at ˜2×10E4 cells per well in a black-walled 96 well plate. Transfection was performed in EMEM with 10% FCS overnight at 100, 10 and 1 nM siRNA complexed with lipofectamine (1.2 ul of lipofectamine per well in 50 ul volume; complexation was performed at room temperature for 15-20 min).

Next day cells were infected with GFP-EBOLA virus (1/50 dilution of stock EBOLA-Zaire GFP, stock E6(4) from 11 Oct. 2005, USAMRIID) in 50 ul of EMEM with 10% FCS. 2 days later cells were fixed in 10% neutral-buffered formalin for >3 days. Formalin was changed before removing from BSL-4 suite. Next formalin was replaced with PBS.

To quantify infection level of cells in individual wells, cells were stained with 10-20 ul/well of 10 ug/ml Hoescht dye and read on Discovery 1 microscope. GFP signal normalized to Hoescht signal was read as a measure of infection level.

Immunofluorescence Ebola-Sudan Assay

VERO cells were transfected at ˜2×10E4 cell per well in a black-walled 96 well plate. Transfection was performed in EMEM with 10% FCS overnight at 100, 10 and 1 nM siRNA complexed with lipofectamine (1.2 ul of lipofectamine per well in 50 ul volume; complexation was performed at room temperature for 15-20 min).

Next day cells were infected with EBOLA-Sudan virus (1/100 dilution of EBOV-Sudan (Boniface), stock GP(1)V(2)E6(2) from 23 May 2006, USAMRIID) in 50 μl of EMEM with 10% FCS. Two days later cells were fixed in 10% neutral-buffered formalin for >3 days. Formalin was changed before removing from BSL-4 suite. Next formalin was replaced with PBS.

To detect infected cells, cells were stained for 4 h at room temperature with mouse anti-Sudan Boniface polyclonal sera (sera was collected from 20 animals and pooled at day 30 post infection of C57BL/6 mice infected with ˜1000 pfu of the EBOLA SUDAN-BONIFACE, stock GP(1) V(2) V(1) E6(2) from 23 May 2006, USAMRIID) at 1:200 dilution in PBS. Then cells were washed with PBS 2× for 5 minutes. Goat anti-mouse IgG-AlexaFluor488 (Molecular Probes) was added at 1:500 dilution in PBS. Cells were washed again with PBS for 5 minutes, 100 ul of PBS was added to each well. To quantify infection level of cells in individual wells, cell were stained with 10-20 ul/well of 10 ug/ml Hoescht dye and read on Discovery 1 microscope. AlexaFluor488 signal normalized to Hoescht signal was read as a measure of infection level.

Plaque Assay for Filoviruses for In Vitro Assay

Vero cells were transfected in 24 well plates at the density of ˜1.5×10E5/well density. Transfection was performed in EMEM with 10% FCS overnight at 100 nM siRNA complexed with lipofectamine (3 ul of lipofectamine per well in 200 ul volume; complexation was performed at room temperature for 15-20 min). Transfection was done in duplicates. 24 hours later duplicate plates were infected in 50 ul/well with either 1/500 diluted Zaire-EBOV [(E6P2) stock from 20 Jun. 2006, USAMRIID] or 1/1000 diluted EBOV-Sudan [(strain Boniface), stock GP(1)V(2)E6(2) from 23 May 2006, USAMRIID]. After 1 hour at 37° C. virus inoculum was replaced with 500 ul of fresh 10% FCS/EMEM.

48-72 h later supernatants were harvested from each well.

Plaque assay was performed with supernatants at 10⁻¹, 10⁻², 10⁻³, 10⁻⁴, 10⁻⁵ and 10⁻⁶ dilutions. Fresh Vero cells in 6-well plates were infected with diluted supernatants for 1 hour at 37° C. with rocking plates every 15 minutes; overlaid with 2 ml/well of 0.5% agarose in EMEM, 5% FCS, Pen/Strep. Six days later plates were overlaid with 2 ml of overlay media+4% neutral red solution and read plates the following day.

siRNA Activity Determination Using the Plasmid System.

Consensus sequences of NP (SEQ ID NO:1043), GP (SEQ ID NO:1044), L, VP24 (SEQ ID NO:1045), VP30 (SEQ ID NO:1046), VP35 (SEQ ID NO:1047), VP40 (SEQ ID NO:1048) were synthesized by GENEART (Regensburg, Germany) and cloned into GENEART standard vector. The L gene was generated as 2 fragments (SEQ ID NO:1049 and SEQ ID NO:1050). All genes were subcloned into individual psiCheck-2 (Promega, Mannheim, Germany) vectors via XhoI and NotI sites, resulting in a construct with the flu gene between the stop-codon and the polyA-signal of Renilla luciferase. Correct cloning was confirmed by end sequencing performed by GATC Biotech (Konstanz, Germany).

Transfections:

Cos-7 cells were seeded at 1.5×10⁴ cells/well on white 96-well plates with clear bottom (Greiner Bio-One GmbH, Frickenhausen, Germany) in 75 μl of growth medium. Directly after seeding the cells, 50 ng of plasmid/well were transfected with Lipofectamine2000 (Invitrogen) as described below for the siRNAs, with the plasmid diluted in Opti-MEM to a final volume of 12.5 μl/well, prepared as a mastermix for the whole plate.

siRNA transfections were performed in quadruplicates 4 h after plasmid transfection. For each well 0.5 μl Lipofectamine2000 (Invitrogen GmbH, Karlsruhe, Germany) were mixed with 12 μl Opti-MEM (Invitrogen) and incubated for 15 min at room temperature. For an siRNA concentration of 50 nM in the 100 μl transfection volume, 1 μl of a 5 μM siRNA were mixed with 11.5 μl Opti-MEM per well, combined with the Lipofectamine2000-Opti-MEM mixture and again incubated for 15 minutes at room temperature. During incubation, the growth medium was removed from cells and replaced by 75 μl/well of fresh medium. siRNA-Lipofectamine2000-complexes were applied completely (25 μl each per well) to the cells and cells were incubated for 24 h at 37° C. and 5% CO₂ in a humidified incubator (Heraeus GmbH, Hanau, Germany).

Cells were harvested by removing growth medium and application of 150 μl of a 1:1 mixture consisting of medium and Dual-Glo Luciferase substrate, from the Dual-Glo Luciferase Assay System (Promega, Mannheim, Germany). The luciferase assay was performed according to the manufacturer's protocol for Dual-Glo Luciferase assay and luminescence was measured in a Victor-Light 1420 Luminescence Counter (Perkin Elmer, Rodgau-Jügesheim, Germany). Values obtained with Renilla luciferase were normalized to the respective values obtained with Firefly luciferase. Values acquired with siRNAs directed against an Ebola gene were normalized to the value obtained with an unspecific siRNA (directed against neomycin resistance gene) set to 100%.

Example 4 In Vivo Filovirus Infection Model

Liposome-formulated siRNAs targeting Ebola genes protected mice from a lethal Ebola virus challenge. Details on the liposome formulation are detailed in the next section. Mice were treated with liposome-formulated siRNA (described below) twice, at 2 hours prior to Ebola infection (5 mg/kg i.v.) and at 3 days after Ebola infection (3 mg/kg i.p.). Mice were infected intraperitoneally with 30,000 LD50 of Ebola-Zaire (LD50 is lethal dose of Ebola infection where 50% of animals die). Mice were monitored for survival with n=10 per treatment group. Negative controls included untreated mice and mice treated with liposome-formulated luciferase siRNA (AD-1955). EK1 is a previously published siRNA sequence targeting the Ebola L gene [Geisbert el al. (2006) The Journal of Infectious Disease 193:1950-1657] that was used as a positive control. The siRNA sequences for EK1 are as follows:

5′ GUACGAAGCUGUAUAUAAAdTdT 3′ (sense) and 5′ UUUAUAUACAGCUUCGUACdTdT 3′ (antisense).

FIG. 1 provides the results. All the negative control-treated animals (untreated and liposomally-formulated luciferase siRNA-treated) died within 6-8 days following Ebola infection. Several of the liposomally-formulated Ebola siRNAs showed significant increases in survival rates compared to the negative controls. Multiple Ebola siRNA (AD-11691, AD-11710, AD-11588, AD-11599, AD-11570) showed more protection against lethal Ebola infection than the previously published EK1 siRNA (FIG. 1).

A further experiment was conducted utilizing one of the active Ebola siRNA (AD-11570) to investigate different dosing routes and treatment regimens. Mice were treated with liposome-formulated Ebola VP35 siRNA (AD-11570) or negative control luciferase siRNA (AD-1955) 2 hours prior to Ebola infection (5 mg/kg i.p.). Mice were infected intraperitoneally with 30,000 LD50 of Ebola-Zaire (LD50 is lethal dose of Ebola infection where 50% of animals die). Mice were monitored for survival with n=10 per treatment group.

FIG. 2 provides the results. The animals treated with lipsomally-formulated AD-11570 showed near complete protection against lethal Ebola infection as compared to the negative control-treated animals (untreated and liposomally-formulated luciferase siRNA-treated) (FIG. 2). These results indicate that a single siRNA administration either via intravenous or intraperitoneal route is able to have a significant impact on survival.

Formulation Procedure

The lipidoid ND98.4HCl (MW 1487) (FIG. 3), Cholesterol (Sigma-Aldrich), and PEG-Ceramide C16 (Avanti Polar Lipids) were used to prepare lipid-siRNA nanoparticles. Stock solutions of each in ethanol were prepared: ND98, 133 mg/mL; Cholesterol, 25 mg/mL, PEG-Ceramide C16, 100 mg/mL. ND98, Cholesterol, and PEG-Ceramide C16 stock solutions were then combined in a 42:48:10 molar ratio. Combined lipid solution was mixed rapidly with aqueous siRNA (in sodium acetate pH 5) such that the final ethanol concentration was 35-45% and the final sodium acetate concentration was 100-300 mM. Lipid-siRNA nanoparticles formed spontaneously upon mixing. Depending on the desired particle size distribution, the resultant nanoparticle mixture was in some cases extruded through a polycarbonate membrane (100 nm cut-off) using a thermobarrel extruder (Lipex Extruder, Northern Lipids, Inc). In other cases, the extrusion step was omitted. Ethanol removal and simultaneous buffer exchange was accomplished by either dialysis or tangential flow filtration. Buffer was exchanged to phosphate buffered saline (PBS) pH 7.2.

Characterization of Formulations

Formulations prepared by either the standard or extrusion-free method are characterized in a similar manner. Formulations are first characterized by visual inspection. They should be whitish translucent solutions free from aggregates or sediment. Particle size and particle size distribution of lipid-nanoparticles are measured by dynamic light scattering using a Malvern Zetasizer Nano ZS (Malvern, USA). Particles should be 20-300 nm, and ideally, 40-100 nm in size. The particle size distribution should be unimodal. The total siRNA concentration in the formulation, as well as the entrapped fraction, is estimated using a dye exclusion assay. A sample of the formulated siRNA is incubated with the RNA-binding dye Ribogreen (Molecular Probes) in the presence or absence of a formulation disrupting surfactant, 0.5% Triton-X100. The total siRNA in the formulation is determined by the signal from the sample containing the surfactant, relative to a standard curve. The entrapped fraction is determined by subtracting the “free” siRNA content (as measured by the signal in the absence of surfactant) from the total siRNA content. Percent entrapped siRNA is typically >85%.

Example 5 siRNAs Targeting Ebola Increased the Life-Span of Mice and Guinea Pigs Infected with Ebola

siRNA directed against different Ebola genes were formulated in liposomes. A single dose of siRNA targeting the VP35 gene (AD-11570) protected both mice and guinea pigs against lethal Ebola infection (1000 PFU; 30000×LD50). Protection was associated with reduction in viral titres and was seen when drug was administered either prophylactically or therapeutically. Irrelevant siRNA (targeting luciferase) similarly formulated showed no protective effect or impact on virus titer.

Studies were conducted in mouse, guinea pig, and nonhuman primate lethal Ebola infection models. The studies are summarized below.

Mouse study 1: Demonstrated efficacy in mouse model of Ebola for multiple siRNA sequences formulated in LNP01. siRNAs were administered by intravenous (i.v.) injection on day 0, followed by intraperitoneal (i.p.) injection on day 3. See FIG. 1.

Mouse study 3: Demonstrated efficacy of siRNA in LNP01 formulation in the mouse model of Ebola when given by either IV or IP route. See FIG. 2. Mice were monitored for survival with n=10 per treatment group.

Mouse study #14: Demonstrated efficacy of siRNA in DODMA in the mouse model of Ebola by the IP route. See FIG. 4. siRNAs were formulated in DODMA:DSPC:Chol:PEG-DMG. Mice were monitored for survival with n=10 per treatment group. Treatment with 10 mg/kg DODMA-formulated AD-11570 siRNAs was also effective to protect guinea pigs infected with Ebola.

Mouse study #15: Demonstrated that siRNA in DODMA formulation is effective down to 0.04 mg/kg in the mouse model of Ebola. AD-11570 consistently gave 25-50% protection, but no clear dose response was seen. The control siRNA AD-1955 gave 25-50% protection, but again, no dose response was observed. See FIG. 5.

Guinea pig study #6: Demonstrated efficacy of multiple doses of siRNA in DODMA formulation in the guinea pig model of Ebola. AD-11570 siRNAs formulated in DODMA:DSPC:Chol:PEG-DMG were effective to protect guinea pigs from Ebola. See FIG. 6.

Guinea pig study #11: Efficacy of siRNAs formulated with DODMA and targeting different Ebola genes in a guinea pig model of Ebola. See FIG. 7

A 95% decrease in viral titers was also observed following administration of LNP01 formulated VP35 siRNA to BALB/c mice (n=5 per group) (FIG. 8). Mice were dosed systemically with LNP01 formulated siRNA at 5 mg/kg i.v. at day 0, then 3 mg/kg i.p. at day 3. Two hours post-siRNA injection at day 0, mice were injected with 1,000 pfu Ebola-Zaire virus and monitored for survival. On day 6 post-infection, the mice were sacrificed and their blood viral titers were determined by plaque assay.

Table 3 shows the results of cell-based and plaque assays.

Table 4 shows the results of plaque assays for control siRNAs.

Table 5 shows the sequences of modified duplexes, and Table 6 shows the effect of the modified duplexes on plaque assay activity and IC₅₀ values in the plasmid-based system.

Table 7 shows the effect of siRNAs on cytokine levels (IFN-alpha and TNF-alpha).

Table 8 shows the siRNA silencing in the plasmid system and calculated IC₅₀ values.

Table 9 shows that nonhuman primates administered siRNAs targeting Ebola did not demonstrate a decrease in lymphocyte or platelet count.

Example 6 Inhibition of Ebola Gene Expression in Humans

A human subject is treated with a pharmaceutical composition comprising a pharmaceutical formulation of an siRNA targeting a Ebola virus gene.

A subject infected with an Ebola virus is selected or identified. The subject can be in need of treatment for diseases caused by Ebola viral infection, such as systemic hemorrhage and multi-organ failure.

At time zero, a suitable first dose of the composition is administered to the subject. The composition is formulated as described herein. After a period of time, the subject's condition is evaluated, e.g., by decrease in symptoms and the like. This measurement can be accompanied by a measurement of Ebola gene expression in said subject, and/or the products of the successful siRNA-targeting of Ebola gene expression. Other relevant criteria can also be measured. The number and strength of doses are adjusted according to the subject's needs.

After treatment, the subject's condition is compared to the condition existing prior to the treatment, or relative to the condition of a similarly afflicted but untreated subject.

Example 7 Protection Against Ebola in Guinea Pigs with LNP09 Formulated AD-11570 Administration

To test of efficacy of siRNAs targeting Ebola genes in protecting guinea pigs from a lethal Ebola virus challenge, the AD-11570 and control siRNA (AD-1955) were formulated in lipid particles containing either DODMA or 2,2-Dilinoleyl-4-dimethylaminoethyl-[1,3]-dioxolane as follows: AD-11570 DODMA, AD-1955 DODMA control, AD-11570 in LNP09, and AD-1955 LNP09 control.

The LNP09 formulation is described above. The DODMA formulation comprises: DODMA (1,2-dioleyloxy-N,N-dimethyl-3-aminopropane) 25.1 mol %; DSPC 20.8 mol %; Cholesterol 44.5 mol %; and PEG-C-DOMG 9.7 mol %.

Forty Hartley guinea pigs, approximately 6 months in age, were used in the study, each with a size of approximately 0.5 kg. Guinea pigs were infected subcutaneously (s.c.) with 100 plaque forming units (PFU) of guinea pig-adapted Ebola-Zaire. Guinea pigs were treated with DODMA or LNP09 formulated siRNA or saline control three times: at 2 hours post infection, 3 days post infection, and 6 days post infection (between 2-3 mg/kg intraperitoneal (i.p.)) (see Table 10 for summary). Guinea pigs were used at n=8 per treatment group. Negative controls included guinea pigs treated with saline and guinea pigs treated with formulated luciferase siRNA (AD-1955). Guinea pigs were monitored for survival (FIG. 9), weight loss (FIG. 10), and general health status.

Results

There were no tolerability issues with LNP09 formulated siRNAs in guinea pigs. In addition, no non-specific virus protection was observed with the LNP09 formulated AD-1955 siRNA control as measured by survival and weight loss of the guinea pigs. Partial virus protection was observed with the LNP09 formulated AD-11570 siRNA compared to controls, as measured by survival and weight loss (See, for example, FIGS. 9 and 10). Less protection was seen with DODMA formulated AD-11570 in this study when compared with previous studies, possibly due to the use of older animals.

Example 8 Dosing Regimen: Protection Against Ebola in Guinea Pigs with LNP09 Formulated AD-11570 Administration

To test the efficacy of siRNAs targeting Ebola genes in protecting guinea pigs from a lethal Ebola virus challenge, the AD-11570 and control siRNA (AD-1955) were formulated in lipid particles containing 2,2-Dilinoleyl-4-dimethylaminoethyl-[1,3]-dioxolane as follows: AD-11570 LNP09 (132 mg) and AD-1955 LNP09 control (96 mg).

The LNP09 formulation is described above.

Forty-eight Hartley guinea pigs were used in the study, each with a size of approximately 0.5 kg and an age of approximately 3 months. Guinea pigs were infected subcutaneously (s.c.) with 100 plaque forming units (PFU) of guinea pig-adapted Ebola-Zaire. Control and drug were administered similar to the previous Example, except for a modified dosing regimen. In this study, some animals (e.g., Group 1) received 3 mg/kg every other day, while others (Groups 2 and 3) received 1 mg/kg daily. Groups 2 and 3 also differed in the timing of the first dose, e.g., Group 1 received a first dose of 3 mg/kg at 2 hours prior to infection, Group 2 received the first dose of 1 mg/kg at 2 hrs prior to infection, and group 3 received the first dose at 30 mins post-infection (Table 11 summarizes the dosing regimen for each group of guinea pigs). Guinea pigs were used at n=8 per treatment group. Negative controls included saline treated guinea pigs and guinea pigs treated with formulated luciferase siRNA (AD-1955). Guinea pigs were monitored for weight loss, general health status, and survival.

The effectiveness of AD-11570 siRNA with respect to the targeting of Ebola genes and the various dosing regimens is demonstrated by the results shown in FIG. 11 and FIG. 12. FIG. 11 shows that AD-11570 siRNA increases survival after two weeks post-infection by roughly 3-7 fold, regardless of the dosage regimen used. At least a 6-fold increase in survival or 75% protection from Ebola virus is observed with the treated animals. FIG. 12 similarly demonstrates that the LNP09/AD-11570 formulation prevents the severe weight loss observed in the absence of treatment. In addition, the siRNA does not appear to be immunostimulatory.

Example 9 Protection Against Ebola in Guinea Pigs with AD-11570 siRNA Administered as Formulation M

To test the efficacy of siRNAs targeting Ebola genes in protecting guinea pigs from a lethal Ebola virus challenge, the AD-11570 and control siRNA (AD-1955) were formulated in lipid particles containing 2,2-Dilinoleyl-4-dimethylaminoethyl-[1,3]-dioxolane as Formulation M, described above. The experimental design was similar to that described in the previous example, except here both the control and test guinea pigs (3 groups, with 6 animals per group) were dosed with 3 mgs/kg siRNA on days 0, 2, 4, and 6 at 3 mg/kg, with the 1st dose given 2 hours prior to infection.

The results are shown in FIG. 13 and FIG. 14. As was observed in the previous Example (using a different formulation), 75% protection against Ebola was observed with the AD-11570 siRNA.

Example 10 Comparison of dsRNA Administration Route and Formulation in Guinea Pigs

To test the efficacy of siRNAs targeting Ebola genes in protecting guinea pigs from a lethal Ebola virus challenge via different administration routes and lipid formulations, the AD-11570 and control siRNA (AD-1955) were formulated in lipid particles containing E/F or P/Q formulation and administered intravenously (1V) or intraperitonealy (IP).

The E/F formulation contains (50%/10%/38.5%/1.5%) of: Cationic Lipid/DSPC/Cholesterol/PEG-C14. The P/Q formulation contains: (30%/30%/38.5%/1.5%) of: Catioinc Lipid/DSPC/Cholesterol/PEG-C14. XTC was the cationic lipid used in this example.

Venous access port (VAP) implanted Hartley guinea pigs (GP) were used in the study (app. 900 grams each). Guinea pigs were infected subcutaneously (s.c.) with 100 plaque forming units (PFU) of guinea pig-adapted Ebola-Zaire. The treatment route was via IV bolus where IV is indicated. The first treatment was given approximately 1 hour prior to infection. Table 12 summarizes the dosing regimen for each group of guinea pigs. Guinea pigs were used at n=3-8 per treatment group. Negative controls included PBS treated guinea pigs and guinea pigs treated with formulated luciferase siRNA (AD-1955). Guinea pigs were monitored for weight loss and survival. The original study design called for equal numbers of GP in all groups, however due to issues with VAP patency, animal numbers had to be adjusted. 4 of the 23 VAPs failed for injection and 1 animal died during surgery. Due to the VAP issues, 3 animals were treated with AD-1955 E/F IV on day 0 and then with AD-11570 P/Q IV on days 1, 2, and 4. Since we could not account for the effect of the day 0 treatment with the AD-1955 E/F formulation on the efficacy of the AD-11570 P/Q formulation, these animals were excluded from further analysis.

The results are shown in FIG. 15 and FIG. 16. 100% protection was observed with the E/F formulation dosed via IV administration. 60% protection was observed with the P/Q formulation dosed via IV administration (N=5). The less efficient protection in the AD-11570 IP treated group that was described above may be due to the use of larger animals in this study (900 grams v. 450 grams) and the larger amount of liposome per animal may exacerbate toxicity seen with the IP route resulting in more mortality. IV treatment shows no evidence for clinical signs of toxicity (e.g., swollen abdomens) observed with the IP treatment and is more efficacious and better tolerated.

Example 11 Dose Response Determination in Guinea Pigs with E/F Formulated AD-11570

To test the efficacy and optimal dose of siRNAs targeting Ebola genes in protecting guinea pigs from a lethal Ebola virus challenge, the AD-11570 and control siRNA (AD-1955) were formulated in lipid particles containing E/F formulation and administered intravenously (IV) at different concentrations.

The E/F formulation is described above. XTC was the cationic lipid used in this example.

VAP implanted Hartley guinea pigs (GP) were used in the study. Guinea pigs were infected subcutaneously (s.c.) with 100 plaque forming units (PFU) of guinea pig-adapted Ebola-Zaire. The treatment route was via IV bolus. The first treatment was given approximately 1 hour prior to infection. Table 13 summarizes the dosing regimen for each group of guinea pigs. Guinea pigs were used at n=6-8 per treatment group. Negative controls included guinea pigs treated with formulated luciferase siRNA (AD-1955). Guinea pigs were monitored for weight loss and survival for 14 days post infection.

The results are shown in FIG. 17 and FIG. 18. Protection with a 3 mg/kg dose was similar to that observed in the above Example. The death of one GP on day 5 was most likely due to heart failure related to the VAP placement and is unlikely to be test article or Ebola infection related. 100% protection was observed with 1 mg/kg dose with no significant weight loss. Partial efficacy was observed with the 0.3 mg/kg dose.

Example 12 Comparison of Different Lipid Formulations in Guinea Pigs with AD-11570

To test the efficacy of differently lipid formulated siRNAs targeting Ebola genes in protecting guinea pigs from a lethal Ebola virus challenge, the AD-11570 was formulated in lipid particles containing Lipid D, Lipid T, or Lipid M formulation and administered intravenously (IV).

All formulations tested in this Example contained 50 mol % of cationic lipid/10% DSPC/38.5% Cholesterol/1.5% PEG-DMG. The Lipid D formulation contained the XTC cationic lipid, described above. The Lipid T formulation contained TechG1, described above. The Lipid M formulation contained MC3, described above.

VAP implanted Hartley guinea pigs (GP) were used in the study. Guinea pigs were infected subcutaneously (s.c.) with 100 plaque forming units (PFU) of guinea pig-adapted Ebola-Zaire. The treatment route was via IV bolus. The first treatment was given approximately 1 hour prior to infection. Table 14 summarizes the dosing regimen for each group of guinea pigs. Guinea pigs were used at n=6-7 per treatment group. Guinea pigs were monitored for weight loss and survival for 15 days post infection.

The results are shown in FIG. 19 and FIG. 20. There was no apparent formulation-related toxicity. There was a lower level of protection with 1 mg/kg Lipid D treatment than observed in the previous Example. It is likely that the larger size of the GPs may be a contributing factor. No substantial protection was observed with Lipid D and Lipid M at 0.3 mg/kg. The 0.3 mg/kg dose of Lipid T provided similar protection as compared to the 1 mg/kg dose of Lipid D. This is consistent with the previously observed improved activity of Lipid T formulations in leukocyte and liver silencing in the mouse model.

Example 13 Post-Ebola Exposure Treatment of Guinea Pits with AD-11570

To test the efficacy of siRNAs targeting Ebola genes in treating guinea pigs after a lethal Ebola virus challenge, the AD-11570 was formulated in lipid particles containing E/F formulation and administered intravenously (IV).

The E/F formulation is described above. XTC was the cationic lipid used in this example.

VAP implanted Hartley guinea pigs (GP) were used in the study. Guinea pigs were infected subcutaneously (s.c.) with 100 plaque forming units (PFU) of guinea pig-adapted Ebola-Zaire. The treatment route was via IV bolus. Table 15 summarizes the dosing regimen for each group of guinea pigs. Guinea pigs were used at n=4-6 per treatment group. Negative controls included guinea pigs treated with PBS via IP administration. Guinea pigs were monitored for weight loss, disease index, and survival for 15 days post infection.

The results are shown in FIG. 21, FIG. 22, and FIG. 23. A 48 hour delay of treatment post-infection provided a level of protection similar to that achieved withtreatment at the time of infection. siRNA treated animals remained largely healthy throughout the study.

Example 14 Viral Load and Disease Pathology Determination in Guinea Pigs with E/F Formulated AD-11570

To test the effect of siRNAs targeting Ebola genes on viral load and disease pathology in guinea pigs, the AD-11570 and control siRNA (AD-1955) were formulated in lipid particles containing E/F formulation and administered intravenously (IV).

The E/F formulation is described above. XTC was the cationic lipid used in this example. The Lipid D formulation contained the XTC cationic lipid, described above.

Guinea pigs (GP) were used in the study. Guinea pigs were infected subcutaneously (s.c.) with 100 plaque forming units (PFU) of guinea pig-adapted Ebola-Zaire. The treatment route was via IV bolus. Table 16 summarizes the dosing regimen for each group of guinea pigs. Guinea pigs were used at n=4-12 per treatment group. Negative controls included guinea pigs treated with formulated luciferase siRNA (AD-1955), PBS, no treatment, and naïve. Guinea pigs were monitored for viral titer, serum chemistry, and pathology on days 5, 7, and 10. Table 17 summarizes the GP sacrifice schedule. Group 4 was used as a control to demonstrate the expected course of infection in naïve animals.

The results are shown in FIG. 24. Treatment with AD-11570 resulted in dramatic suppression of Ebola virus in the GP model. Only 1 of 10 animals treated with AD-11570 had measurable serum viremia at any of the timepoints examined (app. 4 log lower viremia than control animals). This demonstrates the anti-viral effect of treatment with Ebola specific siRNA. Evidence of liver enzyme elevations in the AD-11570 treated animals was observed. This may be related to formulation toxicity or a low level infection in the liver and is consistent with weight loss that typically accompanies XTC treatment in this model. Evidence of maintenance of platelet levels with AD-11570 treatment was observed.

Although methods and materials similar or equivalent to those described herein can be used in the practice or testing of the invention, suitable methods and materials are described below. All publications, patent applications, patents, and other references mentioned herein are incorporated by reference in their entirety. In case of conflict, the present specification, including definitions, will control. In addition, the materials, methods, and examples are illustrative only and not intended to be limiting.

TABLE 2 double overhang design position sense strand antisense strand in Seq Seq duplex target Target Name ID sequence (5′-3′) name ID sequence (5′-3′) name  3-21 VP35 A18480    1 GAUGAAGAUUAAAACCUUCTsT A18481    2 GAAGGUUUUAAUCUUCAUCTsT AD- 11542  4-22 VP35 A18482    3 AUGAAGAUUAAAACCUUCATsT A18483    4 UGAAGGUUUUAAUCUUCAUTsT AD- 11543  5-23 VP35 A18484    5 UGAAGAUUAAAACCUUCAUTsT A18485    6 AUGAAGGUUUUAAUCUUCATsT AD- 11544  6-24 VP35 A18486    7 GAAGAUUAAAACCUUCAUCTsT A18487    8 GAUGAAGGUUUUAAUCUUCTsT AD- 11545 1354-1372 VP35 A18488    9 UGAUGAAGAUUAAGAAAAATsT A18489   10 UUUUUCUUAAUCUUCAUCATsT AD- 11546  7-25 VP35 A18490   11 AAGAUUAAAACCUUCAUCATsT A18491   12 UGAUGAAGGUUUUAAUCUUTsT AD- 11547  8-26 VP35 A18492   13 AGAUUAAAACCUUCAUCAUTsT A18493   14 AUGAUGAAGGUUUUAAUCUTsT AD- 11548  9-27 VP35 A18494   15 GAUUAAAACCUUCAUCAUCTsT A18495   16 GAUGAUGAAGGUUUUAAUCTsT AD- 11549 10-28 VP35 A18496   17 AUUAAAACCUUCAUCAUCCTsT A18497   18 GGAUGAUGAAGGUUUUAAUTsT AD- 11550 11-29 VP35 A18498   19 UUAAAACCUUCAUCAUCCUTsT A18499   20 AGGAUGAUGAAGGUUUUAATsT AD- 11551 12-30 VP35 A18500   21 UAAAACCUUCAUCAUCCUUTsT A18501   22 AAGGAUGAUGAAGGUUUUATsT AD- 11552  1-19 VP30 A18502   23 GAUGAAGAUUAAGAAAAAGTsT A18503   24 CUUUUUCUUAAUCUUCAUCTsT AD- 11553  3-21 VP35 A18504  151 GAuGAAGAuuAAAAccuucTsT A18505  152 GAAGGUUUuAAUCUUcAUCTsT AD- 11554  4-22 VP35 A18506  153 AuGAAGAuuAAAAccuucATsT A18507  154 UGAAGGUUUuAAUCUUcAUTsT AD- 11555  5-23 VP35 A18508  155 uGAAGAuuAAAAccuucAuTsT A18509  156 AUGAAGGUUUuAAUCUUcATsT AD- 11556  6-24 VP35 A18510  157 GAAGAuuAAAAccuucAucTsT A18511  158 GAUGAAGGUUUuAAUCUUCTsT AD- 11557 1354-1372 VP35 A18512  159 uGAuGAAGAuuAAGAAAAATsT A18513  160 UUUUUCUuAAUCUUcAUcATsT AD- 11558  7-25 VP35 A18514  161 AAGAuuAAAAccuucAucATsT A18515  162 UGAUGAAGGUUUuAAUCUUTsT AD- 11559  8-26 VP35 A18516  163 AGAuuAAAAccuucAucAuTsT A18517  164 AUGAUGAAGGUUUuAAUCUTsT AD- 11560  9-27 VP35 A18518  165 GAuuAAAAccuucAucAucTsT A18519  166 GAUGAUGAAGGUUUuAAUCTsT AD- 11561 10-28 VP35 A18520  167 AuuAAAAccuucAucAuccTsT A18521  168 GGAUGAUGAAGGUUUuAAUTsT AD- 11562 11-29 VP35 A18522  169 uuAAAAccuucAucAuccuTsT A18523  170 AGGAUGAUGAAGGUUUuAATsT AD- 11563 12-30 VP35 A18524  171 uAAAAccuucAucAuccuuTsT A18525  172 AAGGAUGAUGAAGGUUUuATsT AD- 11564  1-19 VP30 A18526  173 GAuGAAGAuuAAGAAAAAGTsT A18527  174 CUUUUUCUuAAUCUUcAUCTsT AD- 11565  3-21 VP35 A18528 1019 GAuGAAGAuuAAAAccuucTsT A18529 1020 GAAGGuuuUAAUCuUcAUCTsT AD- 11566  4-22 VP35 A18530 1021 AuGAAGAuuAAAAccuucATsT A18531 1022 uGAAGGuuuUAAUCuUcAUTsT AD- 11567  5-23 VP35 A18532 1023 uGAAGAuuAAAAccuucAuTsT A18533 1024 AuGAAGGuuuuAAUCuUcATsT AD- 11568  6-24 VP35 A18534 1025 GAAGAuuAAAAccuucAucTsT A18535 1026 GAuGAAGGuuuuAAUCuUCTsT AD- 11569 1354-1372 VP35 A18536 1027 uGAuGAAGAuuAAGAAAAATsT A18537 1028 uuuuUCuuAAUCuUcAUcATsT AD- 11570  7-25 VP35 A18538 1029 AAGAuuAAAAccuucAucATsT A18539 1030 uGAuGAAGGuuuuAAUCuUTsT AD- 11571  8-26 VP35 A18540 1031 AGAuuAAAAccuucAucAuTsT A18541 1032 AuGAuGAAGGuuuuAAUCUTsT AD- 11572  9-27 VP35 A18542 1033 GAuuAAAAccuucAucAucTsT A18543 1034 GAuGAuGAAGGuuuuAAUCTsT AD- 11573 10-28 VP35 A18544 1035 AuuAAAAccuucAucAuccTsT A18545 1036 GGAuGAuGAAGGuuuuAAUTsT AD- 11574 11-29 VP35 A18546 1037 uuAALAccuucAucAuccuTsT A18547 1038 AGGAuGAuGAAGGuuuuAATsT AD- 11575 12-30 VP35 A18548 1039 uAAAAccuucAucAuccuuTsT A18549 1040 AAGGAuGAuGAAGGuuuuATsT AD- 11576  1-19 VP30 A18550 1041 GAuGAAGAuuAAGAAAAAGTsT A18551 1042 CuuuuUCuuAAUCuUcAUCTsT AD- 11577  996-1014 NP A18552   25 UGGACACAUGAUGGUGAUCTsT A18553   26 GAUCACCAUCAUGUGUCCATsT AD- 11578 1467-1485 NP A18554   27 AAGCAACUCCAACAAUAUGTsT A18555   28 CAUAUUGUUGGAGUUGCUUTsT AD- 11579 11-29 VP35 A18556   29 AAAACCUUCAUCAUCCUUUTsT A18557   30 AAAGGAUGAUGAAGGUUUUTsT AD- 11580 1357-1375 VP35 A18558   31 UUGAUGAAGAUUAAGAAAATsT A18559   32 UUUUCUUAAUCUUCAUCAATsT AD- 11581  1-19 VP40 A18560   33 GAUGAAGAUUAAGAAAAAGTsT A18561   34 CUUUUUCUUAAUCUUCAUCTsT AD- 11582 647-665 VP40 A18562   35 CCCUGCUGCAACAUGGACATsT A18563   36 UGUCCAUGUUGCAGCAGGGTsT AD- 11583  2-20 VP30 A18564   37 AUGAAGAUUAAGAAAAAGUTsT A18565   38 ACUUUUUCUUAAUCUUCAUTsT AD- 11584  1-19 L A18566   39 AAGAUUAAGAAAAAGUCCATsT A18567   40 UGGACUUUUUCUUAAUCUUTsT AD- 11585  5-23 NP A18568   41 AAGAUUAAUAAUUUUCCUCTsT A18569   42 GAGGAAAAUUAUUAAUCUUTsT AD- 11586 823-841 NP A18570   43 AUGCCGGAAGAGGAGACAATsT A18571   44 UUGUCUCCUCUUCCGGCAUTsT AD- 11587 824-842 NP A18572   45 UGCCGGAAGAGGAGACAACTsT A18573   46 GUUGUCUCCUCUUCCGGCATsT AD- 11588  987-1005 NP A18574   47 GCAAUCAGUAGGACACAUGTsT A18575   48 CAUGUGUCCUACUGAUUGCTsT AD- 11589  988-1006 NP A18576   49 CAAUCAGUAGGACACAUGATsT A18577   50 UCAUGUGUCCUACUGAUUGTsT AD- 11590  989-1007 NP A18578   51 AAUCAGUAGGACACAUGAUTsT A18579   52 AUCAUGUGUCCUACUGAUUTsT AD- 11591  990-1008 NP A18580   53 AUCAGUAGGACACAUGAUGTsT A18581   54 CAUCAUGUGUCCUACUGAUTsT AD- 11592  991-1009 NP A18582   55 UCAGUAGGACACAUGAUGGTsT A18583   56 CCAUCAUGUGUCCUACUGATsT AD- 11593  992-1010 NP A18584   57 CAGUAGGACACAUGAUGGUTsT A18585   58 ACCAUCAUGUGUCCUACUGTsT AD- 11594  993-1011 NP A18586   59 AGUAGGACACAUGAUGGUGTsT A18587   60 CACCAUCAUGUGUCCUACUTsT AD- 11595  994-1012 NP A18588   61 GUAGGACACAUGAUGGUGATsT A18589   62 UCACCAUCAUGUGUCCUACTsT AD- 11596  995-1013 NP A18590   63 UAGGACACAUGAUGGUGAUTsT A18591   64 AUCACCAUCAUGUGUCCUATsT AD- 11597 1005-1023 NP A18592   65 GAUGGUGAUUUUCCGUUUGTsT A18593   66 CAAACGGAAAAUCACCAUCTsT AD- 11598 1006-1024 NP A18594   67 AUGGUGAUUUUCCGUUUGATsT A18595   68 UCAAACGGAAAAUCACCAUTsT AD- 11599 1007-1025 NP A18596   69 UGGUGAUUUUCCGUUUGAUTsT A18597   70 AUCAAACGGAAAAUCACCATsT AD- 11600 1008-1026 NP A18598   71 GGUGAUUUUCCGUUUGAUGTsT A18599   72 CAUCAAACGGAAAAUCACCTsT AD- 11601 1462-1480 NP A18600   73 GCUGAGAAGCAACUCCAACTsT A18601   74 GUUGGAGUUGCUUCUCAGCTsT AD- 11602 1463-1481 NP A18602   75 CUGAGAAGCAACUCCAACATsT A18603   76 UGUUGGAGUUGCUUCUCAGTsT AD- 11603 1464-1482 NP A18604   77 UGAGAAGCAACUCCAACAATsT A18605   78 UUGUUGGAGUUGCUUCUCATsT AD- 11604 1465-1483 NP A18606   79 GAGAAGCAACUCCAACAAUTsT A18607   80 AUUGUUGGAGUUGCUUCUCTsT AD- 11605 1466-1484 NP A18608   81 AGAAGCAACUCCAACAAUATsT A18609   82 UAUUGUUGGAGUUGCUUCUTsT AD- 11606 1353-1371 VP35 A18610   83 AAAAGUGAUGAAGAUUAAGTsT A18611   84 CUUAAUCUUCAUCACUUUUTsT AD- 11607 1354-1372 VP35 A18612   85 AAAGUGAUGAAGAUUAAGATsT A18613   86 UCUUAAUCUUCAUCACUUUTsT AD- 11608 1355-1373 VP35 A18614   87 AAGUGAUGAAGAUUAAGAATsT A18615   88 UUCUUAAUCUUCAUCACUUTsT AD- 11609 1356-1374 VP35 A18616   89 AGUGAUGAAGAUUAAGAAATsT A18617   90 UUUCUUAAUCUUCAUCACUTsT AD- 11610 645-663 VP40 A18618   91 CUGCCUGCUGCAACAUGGATsT A18619   92 UCCAUGUUGCAGCAGGCAGTsT AD- 11611 646-664 VP40 A18620   93 UGCCUGCUGCAACAUGGACTsT A18621   94 GUCCAUGUUGCAGCAGGCATsT AD- 11612 451-469 GP A18622   95 GGCUGAAAACUGCUACAAUTsT A18623   96 AUUGUAGCAGUUUUCAGCCTsT AD- 11613 452-470 GP A18624   97 GCUGAAAACUGCUACAAUCTsT A18625   98 GAUUGUAGCAGUUUUCAGCTsT AD- 11614 453-471 GP A18626   99 CUGAAAACUGCUACAAUCUTsT A18627  100 AGAUUGUAGCAGUUUUCAGTsT AD- 11615 454-472 GP A18628  101 UGAAAACUGCUACAAUCUUTsT A18629  102 AAGAUUGUAGCAGUUUUCATsT AD- 11616 455-473 GP A18630  103 GAAAACUGCUACAAUCUUGTsT A18631  104 CAAGAUUGUAGCAGUUUUCTsT AD- 11617 456-474 GP A18632  105 AAAACUGCUACAAUCUUGATsT A18633  106 UCAAGAUUGUAGCAGUUUUTsT AD- 11618 457-475 GP A18634  107 AAACUGCUACAAUCUUGAATsT A18635  108 UUCAAGAUUGUAGCAGUUUTsT AD- 11619 458-476 GP A18636  109 AACUGCUACAAUCUUGAAATsT A18637  110 UUUCAAGAUUGUAGCAGUUTsT AD- 11620 459-477 GP A18638  111 ACUGCUACAAUCUUGAAAUTsT A18639  112 AUUUCAAGAUUGUAGCAGUTsT AD- 11621 599-617 VP30 A18640  113 AGCAAAUCCAACGGCUGAUTsT A18641  114 AUCAGCCGUUGGAUUUGCUTsT AD- 11622 600-618 VP30 A18642  115 GCAAAUCCAACGGCUGAUGTsT A18643  116 CAUCAGCCGUUGGAUUUGCTsT AD- 11623 601-619 VP30 A18644  117 CAAAUCCAACGGCUGAUGATsT A18645  118 UCAUCAGCCGUUGGAUUUGTsT AD- 11624 135-153 L A18646  119 UUGGACCAAUGUGACCUAGTsT A18647  120 CUAGGUCACAUUGGUCCAATsT AD- 11625 136-154 L A18648  121 UGGACCAAUGUGACCUAGUTsT A18649  122 ACUAGGUCACAUUGGUCCATsT AD- 11626 2100-2118 L A18650  123 AUGCAUGUCAGUGAUUAUUTsT A18651  124 AAUAAUCACUGACAUGCAUTsT AD- 11627 2101-2119 L A18652  125 UGCAUGUCAGUGAUUAUUATsT A18653  126 UAAUAAUCACUGACAUGCATsT AD- 11628 2102-2120 L A18654  127 GCAUGUCAGUGAUUAUUAUTsT A18655  128 AUAAUAAUCACUGACAUGCTsT AD- 11629 2103-2121 L A18656  129 CAUGUCAGUGAUUAUUAUATsT A18657  130 UAUAAUAAUCACUGACAUGTsT AD- 11630 2104-2122 L A18658  131 AUGUCAGUGAUUAUUAUAATsT A18659  132 UUAUAAUAAUCACUGACAUTsT AD- 11631 2114-2132 L A18660  133 UUAUUAUAAUCCACCACAUTsT A18661  134 AUGUGGUGGAUUAUAAUAATsT AD- 11632 2115-2133 L A18662  135 UAUUAUAAUCCACCACAUATsT A18663  136 UAUGUGGUGGAUUAUAAUATsT AD- 11633 2116-2134 L A18664  137 AUUAUAAUCCACCACAUAATsT A18665  138 UUAUGUGGUGGAUUAUAAUTsT AD- 11634 2412-2430 L A18666  139 AAAGUUACAAGUGCCUGUGTsT A18667  140 CACAGGCACUUGUAACUUUTsT AD- 11635 2413-2431 L A18668  141 AAGUUACAAGUGCCUGUGGTsT A18669  142 CCACAGGCACUUGUAACUUTsT AD- 11636 2466-2484 L A18670  143 UCAGGUUUUAUCUAUUUUGTsT A18671  144 CAAAAUAGAUAAAACCUGATsT AD- 11637 2467-2485 L A18672  145 CAGGUUUUAUCUAUUUUGGTsT A18673  146 CCAAAAUAGAUAAAACCUGTsT AD- 11638 2556-2574 L A18674  147 UCUGAUGCAAUUUUUGAUGTsT A18675  148 CAUCAAAAAUUGCAUCAGATsT AD- 11639 2557-2575 L A18676  149 CUGAUGCAAUUUUUGAUGATsT A18677  150 UCAUCAAAAAUUGCAUCAGTsT AD- 11640 1825-1843 NP A18678  151 AGuuAcucGGAAAAcGGcATsT A18679  152 UGCCGUUUUCCGAGuAACUTsT AD- 11641 1588-1606 NP A18680  153 AAcGcuAuGGuAAcucuAATsT A18681  154 UuAGAGUuACcAuAGCGUUTsT AD- 11642 1827-1845 NP A18682  155 uuAcucGGAAAAcGGcAuGTsT A18683  156 cAUGCCGUUUUCCGAGuAATsT AD- 11643 1583-1601 NP A18684  157 AAAcAAAcGcuAuGGuAAcTsT A18685  158 GUuACcAuAGCGUUUGUUUTsT AD- 11644 1488-1506 NP A18686  159 AGAGucucGcGAAcuuGAcTsT A18687  160 GUcAAGUUCGCGAGACUCUTsT AD- 11645 1489-1507 NP A18688  161 GAGucucGcGAAcuuGAccTsT A18689  162 GGUcAAGUUCGCGAGACUCTsT AD- 11646 1585-1603 NP A18690  163 AcAAAcGcuAuGGuAAcucTsT A18691  164 GAGUuACcAuAGCGUUUGUTsT AD- 11647 1586-1604 NP A18692  165 cAAAcGcuAuGGuAAcucuTsT A18693  166 AGAGUuACcAuAGCGUUUGTsT AD- 11648 2231-2249 NP A18694  167 cAccGGcucccGuAuAcAGTsT A18695  168 CUGuAuACGGGAGCCGGUGTsT AD- 11649 2873-2891 NP A18696  169 cuAAcuAGcGAuuuAucuATsT A18697  170 uAGAuAAAUCGCuAGUuAGTsT AD- 11650 1172-1190 VP35 A18698  171 GcuGAAcuAuAGGGuAcGuTsT A18699  172 ACGuACCCuAuAGUUcAGCTsT AD- 11651 1176-1194 VP35 A18700  173 AAcuAuAGGGuAcGuuAcATsT A18701  174 UGuAACGuACCCuAuAGUUTsT AD- 11652 1174-1192 VP35 A18702  175 uGAAcuAuAGGGuAcGuuATsT A18703  176 uAACGuACCCuAuAGUUcATsT AD- 11653 1178-1196 VP35 A18706  177 cuAuAGGGuAcGuuAcAuuTsT A18707  178 AAUGuAACGuACCCuAuAGTsT AD- 11655 251-269 VP35 A18704  179 GGAuuAuGcuAcGcAucccTsT A18705  180 GGGAUGCGuAGcAuAAUCCTsT AD- 11654 416-434 VP35 A18708  181 uuAGAAcAAcGcAuuAcGATsT A18709  182 UCGuAAUGCGUUGUUCuAATsT AD- 11656 421-439 VP35 A18710  183 AcAAcGcAuuAcGAGucuuTsT A18711  184 AAGACUCGuAAUGCGUUGUTsT AD- 11657 1057-1075 VP35 A18712  185 uGAucGAGGuuGGGuAuGuTsT A18713  186 AcAuACCcAACCUCGAUcATsT AD- 11658 167-185 GP A18714  187 ccucGuGAucGAuucAAGATsT A18715  188 UCUUGAAUCGAUcACGAGGTsT AD- 11659 163-181 GP A18716  189 GuuAccucGuGAucGAuucTsT A18717  190 GAAUCGAUcACGAGGuAACTsT AD- 11660 658-676 GP A18720  191 AAcGAcuuucGcuGAAGGuTsT A18721  192 ACCUUcAGCGAAAGUCGUUTsT AD- 11662 755-773 GP A18722  193 AcGGAGGAcccGucuAGuGTsT A18723  194 cACuAGACGGGUCCUCCGUTsT AD- 11663 966-984 GP A18724  195 AGGucAAccccGAAAuuGATsT A18725  196 UcAAUUUCGGGGUUGACCUTsT AD- 11664 978-996 GP A18726  197 AAAuuGAuAcAAcAAucGGTsT A18727  198 CCGAUUGUUGuAUcAAUUUTsT AD- 11665  985-1003 GP A18728  199 uAcAAcAAucGGGGAGuGGTsT A18729  200 CcACUCCCCGAUUGUUGuATsT AD- 11666 1101-1119 GP A18730  201 AGAGuccGGcGcGAAcuucTsT A18731  202 GAAGuUCGCGCCGGACUCUTsT AD- 11667 1730-1748 GP A18718  203 uGGAuAccAuAuuucGGGcTsT A18719  204 GCCCGAAAuAUGGuAUCcATsT AD- 11661 1820-1838 GP A18732  205 cuGGccAAcGAGAcGAcucTsT A18733  206 GAGUCGUCUCGUUGGCcAGTsT AD- 11668 1298-1316 VP30 A18734  207 uAucGcucGuAAuAuAAccTsT A18735  208 GGUuAuAUuACGAGCGAuATsT AD- 11669 295-313 VP30 A18736  209 uucGAGcAcGAucAucAucTsT A18737  210 GAuGAuGAUCGuGCUCGAATsT AD- 11670 590-608 VP30 A18738  211 cucGcGcuuAGcAAAuccATsT A18739  212 UGGAUUUGCuAAGCGCGAGTsT AD- 11671 519-537 VP30 A18740  213 uuAcuccuAcuAAucGcccTsT A18741  214 GGGCGAUuAGuAGGAGuAATsT AD- 11672 126-144 VP30 A18742  215 cuGcGAAccGGuAGAGuuuTsT A18743  216 AAACUCuACCGGUUCGcAGTsT AD- 11673 133-151 VP30 A18744  217 ccGGuAGAGuuuAGuuGcATsT A18745  218 UGcAACuAAACUCuACCGGTsT AD- 11674 292-310 VP30 A18746  219 AuGuucGAGcAcGAucAucTsT A18747  220 GAUGAUCGUGCUCGAAcAUTsT AD- 11675 321-339 VP30 A18748  221 AAuuAucGAGGuGAGuAccTsT A18749  222 GGuACUcACCUCGAuAAUUTsT AD- 11676 910-928 VP30 A18750  223 GGGAccGAcAAucccuAAuTsT A18751  224 AUuAGGGAUUGUCGGUCCCTsT AD- 11677 1295-1313 VP30 A18752  225 ucGuAucGcucGuAAuAuATsT A18753  226 uAuAUuACGAGCGAuACGATsT AD- 11678 331-349 VP30 A18754  227 GuGAGuAccGucAAucAAGTsT A18755  228 CUUGAUUGACGGuACUcACTsT AD- 11679 123-141 VP30 A18756  229 GAucuGcGAAccGGuAGAGTsT A18757  230 CUCuACCGGUUCGcAGAUCTsT AD- 11680 124-142 VP30 A18758  231 AucuGcGAAccGGuAGAGuTsT A18759  232 ACUCuACCGGUUCGcAGAUTsT AD- 11681 1293-1311 VP30 A18760  233 ucucGuAucGcucGuAAuATsT A18761  234 uAUuACGAGCGAuACGAGATsT AD- 11682 145-163 VP30 A18762  235 AGuuGcAAccuAAcAcAcATsT A18763  236 UGUGUGUuAGGUUGcAACUTsT AD- 11683 293-311 VP30 A18764  237 uGuucGAGcAcGAucAucATsT A18765  238 UGAUGAUCGUGCUCGAAcATsT AD- 11684 358-376 VP30 A18766  239 cAcAAGuGcGcGuuccuAcTsT A18767  240 GuAGGAACGCGcACUUGUGTsT AD- 11685 359-377 VP30 A18768  241 AcAAGuGcGcGuuccuAcuTsT A18769  242 AGuAGGAACGCGcACUUGUTsT AD- 11686 518-536 VP30 A18770  243 AuuAcuccuAcuAAucGccTsT A18771  244 GGCGAUuAGuAGGAGuAAUTsT AD- 11687 520-538 VP30 A18772  245 uAcuccuAcuAAucGcccGTsT A18773  246 CGGGCGAUuAGuAGGAGuATsT AD- 11688 524-542 VP30 A18774  247 ccuAcuAAucGcccGuAAGTsT A18775  248 CUuACGGGCGAUuAGuAGGTsT AD- 11689 525-543 VP30 A18776  249 cuAcuAAucGcccGuAAGATsT A18777  250 UCUuACGGGCGAUuAGuAGTsT AD- 11690 584-602 VP30 A18778  251 cAAGGAcucGcGcuuAGcATsT A18779  252 UGCuAAGCGCGAGUCCUUGTsT AD- 11691 469-487 VP24 A18784  253 AGcuAcGGGAcGAuAcAAuTsT A18785  254 AUUGuAUCGUCCCGuAGCUTsT AD- 11694 910-928 VP24 A18786  255 GucGuuGAuucGAuccAAuTsT A18787  256 AUUGGAUCGAAUcAACGACTsT AD- 11695 467-485 VP24 A18788  257 AAAGcuAcGGGAcGAuAcATsT A18789  258 UGuAUCGUCCCGuAGCUUUTsT AD- 11696 862-880 VP24 A18792  259 cAAcAuGcGAAcAcAAcGuTsT A18793  260 ACGUUGUGUUCGcAUGUUGTsT AD- 11698 466-484 VP24 A18796  261 uAAAGcuAcGGGAcGAuAcTsT A18797  262 GuAUCGUCCCGuAGCUUuATsT AD- 11700 523-541 VP24 A18804  263 uGucuuAAGcGAccucuGuTsT A18805  264 AcAGAGGUCGCUuAAGAcATsT AD- 11704 958-976 VP24 A18806  265 ucuAcAuGucGuGAAcuAcTsT A18807  266 GuAGUUcACGAcAUGuAGATsT AD- 11705 959-977 VP24 A18808  267 cuAcAuGucGuGAAcuAcATsT A18809  268 UGuAGUUcACGAcAUGuAGTsT AD- 11706 971-989 VP24 A18810  269 AAcuAcAAcGGAuuGuuGATsT A18811  270 UcAAcAAUCCGUUGuAGUUTsT AD- 11707 1071-1089 VP24 A18812  271 ccGAcAAAucGGcAAuGAATsT A18813  272 UUcAUUGCCGAUUUGUCGGTsT AD- 11708 5886-5904 L A18816  273 AGAucGAAAuuGuAcGAAGTsT A18817  274 CUUCGuAcAAUUUCGAUCUTsT AD- 11710 192-210 L A18818  275 AAuccGcAAcuAcGcAAcuTsT A18819  276 AGUUGCGuAGUUGCGGAUUTsT AD- 11711 5395-5413 L A18820  277 cAcGccAAuuAAcGucAucTsT A18821  278 GAUGACGUuAAUUGGCGUGTsT AD- 11712 193-211 L A18822  279 AuccGcAAcuAcGcAAcuGTsT A18823  280 cAGUUGCGuAGUUGCGGAUTsT AD- 11713 219-237 L A18824  281 ccGAAAcAuAucuAccGuuTsT A18825  282 AACGGuAGAuAUGUUUCGGTsT AD- 11714 2840-2858 L A18826  283 uuucuAccGGAAucuAGGATsT A18827  284 UCCuAGAUUCCGGuAGAAATsT AD- 11715 4779-4797 L A18828  285 AuuAAucGcGGAAcAAuuGTsT A18829  286 cAAUUGUUCCGCGAUuAAUTsT AD- 11716 5275-5293 L A18830  287 AuuucGAucGAucGAGAcATsT A18831  288 uGUCUCGAUCGAUCGAAAUTsT AD- 11717 5391-5409 L A18832  289 GGGAcAcGccAAuuAAcGuTsT A18833  290 ACGUuAAUUGGCGUGUCCCTsT AD- 11718 191-209 L A18834  291 uAAuccGcAAcuAcGcAAcTsT A18835  292 GUUGCGuAGUUGCGGAUuATsT AD- 11719 1614-1632 L A18836  293 AGuAcuAAAcGuGuAccGGTsT A18837  294 CCGGuAcACGUUuAGuACUTsT AD- 11720 4588-4606 L A18838  295 cAcAucGcucAuuGcGAAuTsT A18839  296 AUUCGcAAUGAGCGAUGUGTsT AD- 11721 4590-4608 L A18840  297 cAucGcucAuuGcGAAuAcTsT A18841  298 GuAUUCGcAAUGAGCGAUGTsT AD- 11722 5884-5902 L A18842  299 AcAGAucGAAAuuGuAcGATsT A18843  300 UCGuAcAAUUUCGAUCUGUTsT AD- 11723 161-179 L A18844  301 AGcuuGcGGGuuAuAuucATsT A18845  302 UGAAuAuAACCCGcAAGCUTsT AD- 11724 778-796 L A18846  303 cuGccGAcGucuuGAuAAuTsT A18847  304 AUuAUcAAGACGUCGGcAGTsT AD- 11725 5446-5464 L A18848  305 AGuAcuuAcGGcAAuuGAGTsT A18849  306 CUcAAUUGCCGuAAGuACUTsT AD- 11726 6297-6315 L A18850  307 AAccucGucGAuucAAAAATsT A18851  308 uuuuuGAAUCGACGAGGuUTsT AD- 11727 5269-5287 L A18852  309 AAcuAAAuuucGAucGAucTsT A18853  310 GAUCGAUCGAAAUUuAGUUTsT AD- 11728 1778-1796 L A18854  311 GccuuAuccGAcucGcAAuTsT A18855  312 AUUGCGAGUCGGAuAAGGCTsT AD- 11729 1780-1798 L A18856  313 cuuAuccGAcucGcAAuGuTsT A18857  314 AcAUUGCGAGUCGGAuAAGTsT AD- 11730 3163-3181 L A18858  315 GucGuuuuGcGGccGAuAuTsT A18859  316 AuAUCGGCCGcAAAACGACTsT AD- 11731 3164-3182 L A18860  317 ucGuuuuGcGGccGAuAucTsT A18861  318 GAuAUCGGCCGcAAAACGATsT AD- 11732 5273-5291 L A18862  319 AAAuuucGAucGAucGAGATsT A18863  320 UCUCGAUCGAUCGAAAuuUTsT AD- 11733 6295-6313 L A18864  321 AuAAccucGucGAuucAAATsT A18865  322 UUUGAAUCGACGAGGUuAUTsT AD- 11734 1702-1720 L A18866  323 uAcuAccAcAAuAucGGAATsT A18867  324 UUCCGAuAUUGUGGuAGuATsT AD- 11735 1781-1799 L A18868  325 uuAuccGAcucGcAAuGuuTsT A18869  326 AAcAUUGCGAGUCGGAuAATsT AD- 11736 5270-5288 L A18870  327 AcuAAAuuucGAucGAucGTsT A18871  328 CGAUCGAUCGAAAUUuAGUTsT AD- 11737 5276-5294 L A18872  329 uuucGAucGAucGAGAcAcTsT A18873  330 GuGUCUCGAUCGAUCGAAATsT AD- 11738 5394-5412 L A18874  331 AcAcGccAAuuAAcGucAuTsT A18875  332 AUGACGUuAAUUGGCGUGUTsT AD- 11739 6242-6260 L A18876  333 AAGuuAuAuccGccuuGGuTsT A18877  334 ACcAAGGCGGAuAuAACUUTsT AD- 11740 182-200 L A18878  335 AuAcucccuuAAuccGcAATsT A18879  336 UUGCGGAUuAAGGGAGuAUTsT AD- 11741 194-212 L A18880  337 uccGcAAcuAcGcAAcuGuTsT A18881  338 AcAGUUGCGuAGUUGCGGATsT AD- 11742 575-593 L A18882  339 ucGAGGAAAcucuAGAucATsT A18883  340 UGAUCuAGAGUUUCCUCGATsT AD- 11743 1565-1583 L A18884  341 uGcAGuAuucGAGccuAAuTsT A18885  342 AUuAGGCUCGAAuACUGcATsT AD- 11744 1566-1584 L A18886  343 GcAGuAuucGAGccuAAuGTsT A18887  344 cAUuAGGCUCGAAuACUGCTsT AD- 11745 1567-1585 L A18888  345 cAGuAuucGAGccuAAuGuTsT A18889  346 AcAUuAGGCUCGAAuACUGTsT AD- 11746 2779-2797 L A18890  347 cAuuGGcAcuAGcGGuAccTsT A18891  348 GGuACCGCuAGUGCcAAUGTsT AD- 11747 2838-2856 L A18892  349 uGuuucuAccGGAAucuAGTsT A18893  350 CuAGAUUCCGGuAGAAAcATsT AD- 11748 2892-2910 L A18894  351 AcuuAucuccGAAuGAuuGTsT A18895  352 cAAUcAUUCGGAGAuAAGUTsT AD- 11749 2981-2999 L A18896  353 AAAuccuAGcGGAuuAAAuTsT A18897  354 AUUuAAUCCGCuAGGAUUUTsT AD- 11750 2982-3000 L A18898  355 AAuccuAGcGGAuuAAAuGTsT A18899  356 cAUUuAAUCCGCuAGGAUUTsT AD- 11751 3038-3056 L A18900  357 GAuuGuAcGcAGGAccAucTsT A18901  358 GAUGGUCCUGCGuAcAAUCTsT AD- 11752 3149-3167 L A18902  359 AAcuccuGuuAuGAGucGuTsT A18903  360 ACGACUcAuAAcAGGAGUUTsT AD- 11753 3168-3186 L A18904  361 uuuGcGGccGAuAucuuuuTsT A18905  362 AAAAGAuAUCGGCCGcAAATsT AD- 11754 3889-3907 L A18906  363 GGuAcAAcGAucAAuAcAGTsT A18907  364 CUGuAUUGAUCGUUGuACCTsT AD- 11755 3922-3940 L A18908  365 uGGccAAucGuAuGAGuAATsT A18909  366 UuACUcAuACGAUUGGCcATsT AD- 11756 4001-4019 L A18910  367 GucuGcAcGcGAcAGcAAuTsT A18911  368 AUUGCUGUCGCGUGcAGACTsT AD- 11757 4584-4602 L A18912  369 cuAccAcAucGcucAuuGcTsT A18913  370 GcAAUGAGCGAUGUGGuAGTsT AD- 11758 4593-4611 L A18914  371 cGcucAuuGcGAAuAcuuATsT A18915  372 uAAGuAUUCGcAAUGAGCGTsT AD- 11759 4598-4616 L A18916  373 AuuGcGAAuAcuuAAGccATsT A18917  374 UGGCUuAAGuAUUCGcAAUTsT AD- 11760 4601-4619 L A18918  375 GcGAAuAcuuAAGccAAcATsT A18919  376 UGUUGGCUuAAGuAUUCGCTsT AD- 11761 4638-4656 L A18920  377 AuGucAcGGuuAAuGAGuATsT A18921  378 uACUcAUuAACCGUGAcAUTsT AD- 11762 4778-4796 L A18922  379 AAuuAAucGcGGAAcAAuuTsT A18923  380 AAUUGUUCCGCGAUuAAUUTsT AD- 11763 5274-5292 L A18924  381 AAuuucGAucGAucGAGAcTsT A18925  382 GUCUCGAUCGAUCGAAAuUTsT AD- 11764 5392-5410 L A18926  383 GGAcAcGccAAuuAAcGucTsT A18927  384 GACGUuAAUUGGCGUGUCCTsT AD- 11765 5649-5667 L A18928  385 AcGcuAGcuAcuGAGuccATsT A18929  386 UGGACUcAGuAGCuAGCGUTsT AD- 11766 5833-5851 L A18930  387 cuAAGcAAGucGAGGuuAuTsT A18931  388 AuAACCUCGACUUGCUuAGTsT AD- 11767 6243-6261 L A18932  389 AGuuAuAuccGccuuGGuuTsT A18933  390 AACcAAGGCGGAuAuAACUTsT AD- 11768 6290-6308 L A18934  391 cAGGuAuAAccucGucGAuTsT A18935  392 AUCGACGAGGUuAuACCUGTsT AD- 11769 6291-6309 L A18936  393 AGGuAuAAccucGucGAuuTsT A18937  394 AAUCGACGAGGUuAuACCUTsT AD- 11770 1816-1834 NP A18938  395 AcuAcGAGGAuucGGcuGATsT A18939  396 UcAGCCGAAUCCUCGuAGUTsT AD- 11771 875-893 NP A18940  397 ucuAcccAAAcuuGucGuuTsT A18941  398 AACGAcAAGUUUGGGuAGATsT AD- 11772 1817-1835 NP A18942  399 cuAcGAGGAuucGGcuGAATsT A18943  400 UUcAGCCGAAUCCUCGuAGTsT AD- 11773 1812-1830 NP A18944  401 ccuGAcuAcGAGGAuucGGTsT A18945  402 CCGAAUCCUCGuAGUcAGGTsT AD- 11774 1819-1837 NP A18946  403 AcGAGGAuucGGcuGAAGGTsT A18947  404 CCUUcAGCCGAAUCCUCGUTsT AD- 11775 2140-2158 NP A18948  405 AcGAGAGucucAcAucccuTsT A18949  406 AGGGAuGuGAGACUCUCGUTsT AD- 11776 730-748 VP35 A18950  407 AAAuuucGGGcGAccuuAcTsT A18951  408 GuAAGGUCGCCCGAAAUUUTsT AD- 11777 735-753 VP35 A18952  409 ucGGGcGAccuuAcAuuucTsT A18953  410 GAAAUGuAAGGUCGCCCGATsT AD- 11778 195-213 VP35 A18954  411 uGAccGGcAAAAuAccGcuTsT A18955  412 AGCGGuAUUUUGCCGGUcATsT AD- 11779 198-216 VP35 A18956  413 ccGGcAAAAuAccGcuAAcTsT A18957  414 GUuAGCGGuAUUUUGCCGGTsT AD- 11780 379-397 VP35 A18958  415 AGcuGuGcGucGGcAAAccTsT A18959  416 GGUUUGCCGACGcAcAGCUTsT AD- 11781 646-664 VP35 A18960  417 AuuGAAAGAuccGAAcGGGTsT A18961  418 CCCGUUCGGAUCUUUcAAUTsT AD- 11782 731-749 VP35 A18962  419 AAuuucGGGcGAccuuAcATsT A18963  420 UGuAAGGUCGCCCGAAAUUTsT AD- 11783 732-750 VP35 A18964  421 AuuucGGGcGAccuuAcAuTsT A18965  422 AUGuAAGGUCGCCCGAAAUTsT AD- 11784 1193-1211 VP35 A18966  423 GucuAuuGuGucAuAAGcuTsT A18967  424 AGCUuAUGAcAcAAuAGACTsT AD- 11785 438-456 VP40 A18968  425 cucGcAucuuAuAcGAucATsT A18969  426 UGAUCGuAuAAGAUGCGAGTsT AD- 11786 1301-1319 VP40 A18970  427 uGcAuAAGcGAuccAuAcuTsT A18971  428 AGuAUGGAUCGCUuAUGcATsT AD- 11787 1191-1209 VP40 A18972  429 AAuGuAcuAAucGGGucAATsT A18973  430 UUGACCCGAUuAGuAcAUUTsT AD- 11788 442-460 VP40 A18974  431 cAucuuAuAcGAucAcccATsT A18975  432 UGGGUGAUCGuAuAAGAUGTsT AD- 11789 443-461 VP40 A18976  433 AucuuAuAcGAucAcccAuTsT A18977  434 AUGGGUGAUCGuAuAAGAUTsT AD- 11790 478-496 VP40 A18978  435 AcccccucGuuAGAGuGAATsT A18979  436 UUcACUCuAACGAGGGGGUTsT AD- 11791 834-852 VP40 A18980  437 AucGuGccAAuuGAuccAGTsT A18981  438 CUGGAUcAAUUGGcACGAUTsT AD- 11792 1192-1210 VP40 A18982  439 AuGuAcuAAucGGGucAAGTsT A18983  440 CUUGACCCGAUuAGuAcAUTsT AD- 11793 1194-1212 VP40 A18984  441 GuAcuAAucGGGucAAGGATsT A18985  442 UCCUUGACCCGAUuAGuACTsT AD- 11794 1300-1318 VP40 A18986  443 AuGcAuAAGcGAuccAuAcTsT A18987  444 GuAUGGAUCGCUuAUGcAUTsT AD- 11795 465-483 GP A18988  445 AcGGGAGcGAAuGcuuAccTsT A18989  446 GGuAAGcAUUCGCUCCCGUTsT AD- 11796 358-376 VP30 A18990  447 AGuuAGAGucccuAcGGuuTsT A18991  448 AACCGuAGGGACUCuAACUTsT AD- 11797 331-349 VP30 A18992  449 cuAccGuAGuAGucGAAGuTsT A18993  450 ACUUCGACuACuACGGuAGTsT AD- 11798 250-268 VP30 A18994  451 GAAuucAcGuGccGAccAGTsT A18995  452 CUGGUCGGcACGUGAAUUCTsT AD- 11799 1009-1027 VP30 A18996  453 uGcccccccAAGcGuuAAuTsT A18997  454 AUuAACGCUUGGGGGGGcATsT AD- 11800 1318-1336 VP30 A18998  455 AGAGuGuuAGGAucGuuAuTsT A18999  456 AuAACGAUCCuAAcACUCUTsT AD- 11801 126-144 VP30 A19000  457 AAucccGAGGcGGcAAuucTsT A19001  458 GAAuuGCCGCCUCGGGAuUTsT AD- 11802 354-372 VP30 A19002  459 cGcAAGuuAGAGucccuAcTsT A19003  460 GuAGGGACUCuAACUUGCGTsT AD- 11803 553-571 VP30 A19004  461 uGAuucAucGcuuAAuAuATsT A19005  462 uAuAUuAAGCGAUGAAUcATsT AD- 11804 583-601 VP30 A19006  463 AGAccuAAGAcuAGcAAAuTsT A19007  464 AUUUGCuAGUCUuAGGUCUTsT AD- 11805 652-670 VP30 A19008  465 AuuAcuAGucGAGAcuGcuTsT A19009  466 AGcAGUCUCGACuAGuAAUTsT AD- 11806  992-1010 VP30 A19010  467 ucAGGccuAcGcuuAcuuGTsT A19011  468 cAAGuAAGCGuAGGCCUGATsT AD- 11807 1013-1031 VP30 A19012  469 cccccAAGcGuuAAuGAAGTsT A19013  470 CUUcAUuAACGCUUGGGGGTsT AD- 11808 404-422 VP24 A19014  471 AuuAuAcGGGuccAuuAAuTsT A19015  472 AUuAAUGGACCCGuAuAAUTsT AD- 11809 888-906 VP24 A19016  473 cucAAcGAGuAAAGGAccATsT A19017  474 UGGUCCUUuACUCGUUGAGTsT AD- 11810 1247-1265 VP24 A19018  475 uuGuAcGAuAGGGcuAAcATsT A19019  476 UGUuAGCCCuAUCGuAcAATsT AD- 11811 536-554 VP24 A19020  477 GuuGuGuuuAGcGAccuAuTsT A19021  478 AuAGGUCGCuAAAcAcAACTsT AD- 11812 1050-1068 VP24 A19022  479 GGAcuAAuAuGGGuuAucuTsT A19023  480 AGAuAACCcAuAUuAGUCCTsT AD- 11813 1095-1113 VP24 A19024  481 cuGcGAuGGAuAuAcGAcATsT A19025  482 UGUCGuAuAUCcAUCGcAGTsT AD- 11814 535-553 VP24 A19026  483 AGuuGuGuuuAGcGAccuATsT A19027  484 uAGGUCGCuAAAcAcAACUTsT AD- 11815 196-214 VP24 A19028  485 uuGAAcuAGucuAcucGcATsT A19029  486 UGCGAGuAGACuAGUUcAATsT AD- 11816 215-233 VP24 A19030  487 GAAuccuAccGGGAAuAGATsT A19031  488 UCuAUUCCCGGuAGGAUUCTsT AD- 11817 403-421 VP24 A19032  489 uAuuAuAcGGGuccAuuAATsT A19033  490 UuAAUGGACCCGuAuAAuATsT AD- 11818 406-424 VP24 A19034  491 uAuAcGGGuccAuuAAuuuTsT A19035  492 AAAUuAAUGGACCCGuAuATsT AD- 11819 1140-1158 VP24 A19036  493 uAcAuGAAucGAcAcuuAATsT A19037  494 UuAAGUGUCGAUUcAUGuATsT AD- 11820 1243-1261 VP24 A19038  495 AAAAuuGuAcGAuAGGGcuTsT A19039  496 AGCCCuAUCGuAcAAUUUUTsT AD- 11821 1249-1267 VP24 A19040  497 GuAcGAuAGGGcuAAcAuuTsT A19041  498 AAUGUuAGCCCuAUCGuACTsT AD- 11822 1590-1608 VP24 A19042  499 GAGcccAAAuuAAcAcGGuTsT A19043  500 ACCGUGUuAAUUUGGGCUCTsT AD- 11823 3688-3706 L A19044  501 cccGcuAuuAAGccGAGGuTsT A19045  502 ACCUCGGCUuAAuAGCGGGTsT AD- 11824 3687-3705 L A19046  503 GcccGcuAuuAAGccGAGGTsT A19047  504 CCUCGGCUuAAuAGCGGGCTsT AD- 11825 2956-2974 L A19048  505 AAuuGuAGcGcAAuuGAcuTsT A19049  506 AGUcAAUUGCGCuAcAAUUTsT AD- 11826 2615-2633 L A19050  507 AGcGAucAAucuccGAAAcTsT A19051  508 GuuUCGGAGAuuGAUCGCUTsT AD- 11827 2612-2630 L A19052  509 uuGAGcGAucAAucuccGATsT A19053  510 UCGGAGAUUGAUCGCUcAATsT AD- 11828 4595-4613 L A19054  511 uucGAAucuucAAAccGAcTsT A19055  512 GUCGGuuuGAAGAuUCGAATsT AD- 11829 2613-2631 L A19056  513 uGAGcGAucAAucuccGAATsT A19057  514 UUCGGAGAUUGAUCGCUcATsT AD- 11830 2614-2632 L A19058  515 GAGcGAucAAucuccGAAATsT A19059  516 uuUCGGAGAuuGAUCGCUCTsT AD- 11831 3941-3959 L A19060  517 cAAcGcGcuuGAuGGuAucTsT A19061  518 GAuACcAUcAAGCGCGUUGTsT AD- 11832 3942-3960 L A19062  519 AAcGcGcuuGAuGGuAucuTsT A19063  520 AGAuACcAUcAAGCGCGUUTsT AD- 11833 1680-1698 L A19064  521 AuAcGcccAAGAAcuuAGGTsT A19065  522 CCuAAGUUCUUGGGCGuAUTsT AD- 11834 3686-3704 L A19066  523 AGcccGcuAuuAAGccGAGTsT A19067  524 CUCGGCUuAAuAGCGGGCUTsT AD- 11835 4255-4273 L A19068  525 uuAucGAuuGAcAGuccuuTsT A19069  526 AAGGACUGUcAAUCGAuAATsT AD- 11836 1374-1392 L A19070  527 AGAccGAuGuuuAAcGccGTsT A19071  528 CGGCGUuAAAcAUCGGUCUTsT AD- 11837 5470-5488 L A19072  529 AccAuAuAuuGucGcuucATsT A19073  530 UGAAGCGAcAAuAuAUGGUTsT AD- 11838 3872-3890 L A19074  531 AuAuuGuGcAucGGuAuAATsT A19075  532 UuAuACCGAUGcAcAAuAUTsT AD- 11839 1384-1402 L A19076  533 uuAAcGccGGGAuuGAAuuTsT A19077  534 AAUUcAAUCCCGGCGUuAATsT AD- 11840 4519-4537 L A19078  535 uGcAcGAAAAAGAucGGAcTsT A19079  536 GUCCGAUCUUUUUCGUGcATsT AD- 11841 3682-3700 L A19080  537 GGucAGcccGcuAuuAAGcTsT A19081  538 GCUuAAuAGCGGGCUGACCTsT AD- 11842 2954-2972 L A19082  539 GGAAuuGuAGcGcAAuuGATsT A19083  540 UcAAUUGCGCuAcAAUUCCTsT AD- 11843 5467-5485 L A19084  541 AcuAccAuAuAuuGucGcuTsT A19085  542 AGCGAcAAuAuAUGGuAGUTsT AD- 11844 1376-1394 L A19086  543 AccGAuGuuuAAcGccGGGTsT A19087  544 CCCGGCGUuAAAcAUCGGUTsT AD- 11845 2448-2466 L A19088  545 uGAuGAGAcuuucGuAcAcTsT A19089  546 GUGuACGAAAGUCUcAUcATsT AD- 11846 1023-1041 L A19090  547 AcGAAAAGGGcGGuuuuuATsT A19091  548 uAAAAACCGCCCUUUUCGUTsT AD- 11847 1377-1395 L A19092  549 ccGAuGuuuAAcGccGGGATsT A19093  550 UCCCGGCGUuAAAcAUCGGTsT AD- 11848 2619-2637 L A19094  551 AucAAucuccGAAAcuAGATsT A19095  552 UCuAGUUUCGGAGAUUGAUTsT AD- 11849 5608-5626 L A19096  553 AAAuAcGGcGuuAAGAAGuTsT A19097  554 ACUUCUuAACGCCGuAUUUTsT AD- 11850 5607-5625 L A19098  555 AAAAuAcGGcGuuAAGAAGTsT A19099  556 CUUCUuAACGCCGuAUUUUTsT AD- 11851 6396-6414 L A19100  557 ucGAAcccAGAcuuAucAuTsT A19101  558 AUGAuAAGUCUGGGUUCGATsT AD- 11852 4165-4183 L A19102  559 AcAAccAcGcuAAAucuAGTsT A19103  560 CuAGAUUuAGCGUGGUUGUTsT AD- 11853 4250-4268 L A19104  561 GcAAcuuAucGAuuGAcAGTsT A19105  562 CUGUcAAUCGAuAAGUUGCTsT AD- 11854 6434-6452 L A19106  563 GAcGGAuAAcuAAAcuAGuTsT A19107  564 ACuAGUUuAGUuAUCCGUCTsT AD- 11855 2959-2977 L A19108  565 uGuAGcGcAAuuGAcuuuGTsT A19109  566 cAAAGUcAAUUGCGCuAcATsT AD- 11856 6433-6451 L A19110  567 GGAcGGAuAAcuAAAcuAGTsT A19111  568 CuAGUUuAGUuAUCCGUCCTsT AD- 11857  83-101 L A19112  569 uGGcuAcccAAcAuAcAcATsT A19113  570 UGUGuAUGUUGGGuAGCcATsT AD- 11858 1382-1400 L A19114  571 GuuuAAcGccGGGAuuGAATsT A19115  572 UUcAAUCCCGGCGUuAAACTsT AD- 11859 1014-1032 NP A19116  573 uuuccGuuuGAuGcGAAcATsT A19117  574 UGUUCGcAUcAAACGGAAATsT AD- 11860 1805-1823 NP A19118  575 GAAGcuAcGGcGAAuAccATsT A19119  576 UGGuAUUCGCCGuAGCUUCTsT AD- 11861 1862-1880 NP A19120  577 uGGuccuAuucGAucuAGATsT A19121  578 UCuAGAUCGAAuAGGACcATsT AD- 11862 1016-1034 NP A19122  579 uccGuuuGAuGcGAAcAAATsT A19123  580 UUUGUUCGcAUcAAACGGATsT AD- 11863 2230-2248 NP A19124  581 ccAccGGcucccGuAuAcATsT A19125  582 UGuAuACGGGAGCCGGUGGTsT AD- 11864 2233-2251 NP A19126  583 ccGGcucccGuAuAcAGAGTsT A19127  584 CUCUGuAuACGGGAGCCGGTsT AD- 11865 959-977 NP A19136  585 AAGGAcuGAuAcAAuAuccTsT A19137  586 GGAuAUUGuAUcAGUCCUUTsT AD- 11870 1017-1035 NP A19138  587 ccGuuuGAuGcGAAcAAAuTsT A19139  588 AUUUGUUCGcAUcAAACGGTsT AD- 11871 2124-2142 NP A19140  589 cccAcuGGAcGAuGccGAcTsT A19141  590 GUCGGcAUCGUCcAGUGGGTsT AD- 11872 745-763 NP A19142  591 cGuGAuGGAGuGAAGcGccTsT A19143  592 GGCGCUUcACUCcAUcACGTsT AD- 11873 2229-2247 NP A19144  593 cccAccGGcucccGuAuAcTsT A19145  594 GuAuACGGGAGCCGGUGGGTsT AD- 11874 2119-2137 NP A20118  595 GcAGAcccAcuGGAcGAuGTsT A20119  596 cAUCGUCcAGUGGGUCUGCTsT AD- 12462 1587-1605 NP A20120  597 AAAcGcuAuGGuAAcucuATsT A20121  598 uAGAGUuACcAuAGCGUUUTsT AD- 12463 1300-1318 NP A20122  599 uucGcccGAcuuuuGAAccTsT A20123  600 GGUUcAAAAGUCGGGCGAATsT AD- 12464 1808-1826 NP A20124  601 GcuAcGGcGAAuAccAGAGTsT A20125  602 CUCUGGuAUUCGCCGuAGCTsT AD- 12465 1813-1831 NP A20126  603 GGcGAAuAccAGAGuuAcuTsT A20127  604 AGuAACUCUGGuAUUCGCCTsT AD- 12466 532-550 VP35 A19146  605 GGuGAuGAcAAccGGucGGTsT A19147  606 CCGACCGGUUGUcAUcACCTsT AD- 11875 417-435 VP35 A19148  607 uAGAAcAAcGcAuuAcGAGTsT A19149  608 CUCGuAAUGCGUUGUUCuATsT AD- 11876 741-759 VP35 A19152  609 GGAAAccuGAcAuuucGGcTsT A19153  610 GCCGAAAUGUcAGGUUUCCTsT AD- 11878 1049-1067 VP35 A19154  611 cccAAGAuuGAucGAGGuuTsT A19155  612 AACCUCGAUcAAUCUUGGGTsT AD- 11879 206-224 VP35 A19160  613 AGAAuuccuGuAAGcGAcATsT A19161  614 UGUCGCUuAcAGGAAUUCUTsT AD- 11882 246-264 VP35 A19162  615 AuccAGGAuuAuGcuAcGcTsT A19163  616 GCGuAGcAuAAUCCUGGAUTsT AD- 11883 247-265 VP35 A19164  617 uccAGGAuuAuGcuAcGcATsT A19165  618 UGCGuAGcAuAAUCCUGGATsT AD- 11884 287-305 VP35 A19166  619 ccAAAcccGAAGAcGcGcATsT A19167  620 uGCGCGUCuUCGGGuuuGGTsT AD- 11885 314-332 VP35 A19168  621 AcccAAAcGGAcccAAuuuTsT A19169  622 AAAuuGGGUCCGuuuGGGUTsT AD- 11886 319-337 VP35 A19170  623 AAcGGAcccAAuuuGcAAuTsT A19171  624 AUUGcAAAUUGGGUCCGUUTsT AD- 11887 414-432 VP35 A19172  625 cAuuAGAAcAAcGcAuuAcTsT A19173  626 GuAAUGCGUUGUUCuAAUGTsT AD- 11888 415-433 VP35 A19174  627 AuuAGAAcAAcGcAuuAcGTsT A19175  628 CGuAAUGCGUUGUUCuAAUTsT AD- 11889 439-457 VP35 A19176  629 uGAGAAuGGucuAAAGccATsT A19177  630 UGGCUUuAGACcAUUCUcATsT AD- 11890 576-594 VP35 A19178  631 AGGcuuAuuGGGccGAAcATsT A19179  632 UGUUCGGCCcAAuAAGCCUTsT AD- 11891 413-431 VP35 A20128  633 ucAuuAGAAcAAcGcAuuATsT A20129  634 uAAUGCGUUGUUCuAAUGATsT AD- 12467 583-601 VP35 A20130  635 uuGGGccGAAcAuGGucAATsT A20131  636 UUGACcAUGUUCGGCCcAATsT AD- 12468  983-1001 VP35 A20132  637 cAcAuccGcucucGAGGuGTsT A20133  638 cACCUCGAGAGCGGAUGUGTsT AD- 12469 318-336 VP35 A20134  639 AAAcGGAcccAAuuuGcAATsT A20135  640 UUGcAAAUUGGGUCCGUUUTsT AD- 12470 420-438 VP35 A20136  641 AAcAAcGcAuuAcGAGucuTsT A20137  642 AGACUCGuAAUGCGUUGUUTsT AD- 12471 419-437 VP35 A20138  643 GAAcAAcGcAuuAcGAGucTsT A20139  644 GACUCGuAAUGCGUUGUUCTsT AD- 12472 134-152 VP35 A20140  645 GccAcGAcucAAAAcGAcATsT A20141  646 UGUCGUUUUGAGUCGUGGCTsT AD- 12473 893-911 VP40 A19180  647 ccAcAAGcuGAccGGuAAGTsT A19181  648 CUuACCGGUcAGCUUGUGGTsT AD- 11892 892-910 VP40 A19182  649 uccAcAAGcuGAccGGuAATsT A19183  650 UuACCGGUcAGCUUGUGGATsT AD- 11893 325-343 VP40 A19188  651 uGAAuGucAuAucGGGcccTsT A19189  652 GGGCCCGAuAUGAcAUUcATsT AD- 11896 450-468 VP40 A19190  653 AcuAucAcccAuuucGGcATsT A19191  654 UGCCGAAAUGGGUGAuAGUTsT AD- 11897 662-680 VP40 A19194  655 GAccGAuGAcAcuccAAcATsT A19195  656 UGUUGGAGUGUcAUCGGUCTsT AD- 11899 200-218 VP40 A19198  657 GAcAccGGAGucAGucAAuTsT A19199  658 AuuGACuGACUCCGGuGUCTsT AD- 11901 203-221 VP40 A19200  659 AccGGAGucAGucAAuGGGTsT A19201  660 CCcAUUGACUGACUCCGGUTsT AD- 11902 204-222 VP40 A19202  661 ccGGAGucAGucAAuGGGGTsT A19203  662 CCCcAUUGACUGACUCCGGTsT AD- 11903 225-243 VP40 A19204  663 AcuccAucGAAuccAcucATsT A19205  664 uGAGuGGAuUCGAuGGAGUTsT AD- 11904 386-404 VP40 A19206  665 uGucGcuGAucAAAAGAccTsT A19207  666 GGUCUUUUGAUcAGCGAcATsT AD- 11905 584-602 VP40 A19208  667 AGuccAAcuAccccAGuAuTsT A19209  668 AuACUGGGGuAGUUGGACUTsT AD- 11906 631-649 VP40 A19210  669 uGAucAcccAAccAcuGccTsT A19211  670 GGcAGUGGUUGGGUGAUcATsT AD- 11907 660-678 VP40 A19212  671 uGGAccGAuGAcAcuccAATsT A19213  672 UUGGAGUGUcAUCGGUCcATsT AD- 11908 663-681 VP40 A19214  673 AccGAuGAcAcuccAAcAGTsT A19215  674 CUGUUGGAGUGUcAUCGGUTsT AD- 11909 929-947 VP40 A19218  675 uGGAcAAccAAucAucccuTsT A19219  676 AGGGAUGAUUGGUUGUCcATsT AD- 11911 1019-1037 VP40 A19220  677 uuGuGAcAcGuGucAuucuTsT A19221  678 AGAAUGAcACGUGUcAcAATsT AD- 11912 243-261 VP40 A19224  679 AGGccAAuuGccGAuGAcATsT A19225  680 UGUcAUCGGcAAUUGGCCUTsT AD- 11914 140-158 VP40 A20142  681 AuAcccuGucAGGucAAAuTsT A20143  682 AUUUGACCUGAcAGGGuAUTsT AD- 12474 141-159 VP40 A20144  683 uAcccuGucAGGucAAAuuTsT A20145  684 AAUUUGACCUGAcAGGGuATsT AD- 12475 378-396 VP40 A20146  685 ccucuAGGuGucGcuGAucTsT A20147  686 GAUcAGCGAcACCuAGAGGTsT AD- 12476 427-445 VP40 A20148  687 ccGccAucAuGcuuGcuucTsT A20149  688 GAAGcAAGcAUGAUGGCGGTsT AD- 12477 898-916 VP40 A20150  689 AGcuGAccGGuAAGAAGGuTsT A20151  690 ACCUUCUuACCGGUcAGCUTsT AD- 12478 199-217 VP40 A20152  691 uGAcAccGGAGucAGucAATsT A20153  692 UUGACUGACUCCGGUGUcATsT AD- 12479 568-586 VP40 A20154  693 AGuucGuucuuccGccAGuTsT A20155  694 ACUGGCGGAAGAACGAACUTsT AD- 12480 569-587 VP40 A20156  695 GuucGuucuuccGccAGucTsT A20157  696 GACUGGCGGAAGAACGAACTsT AD- 12481 1728-1746 GP A19232  697 ccuGGAuAccAuAuuucGGTsT A19233  698 CCGAAAuAUGGuAUCcAGGTsT AD- 11918 1729-1747 GP A19234  699 cuGGAuAccAuAuuucGGGTsT A19235  700 CCCGAAAuAUGGuAUCcAGTsT AD- 11919 1818-1836 GP A19246  701 AGcuGGccAAcGAGAcGAcTsT A19247  702 GUCGUCUCGUUGGCcAGCUTsT AD- 11925 1821-1839 GP A19248  703 uGGccAAcGAGAcGAcucATsT A19249  704 UGAGUCGUCUCGUUGGCcATsT AD- 11926 1732-1750 GP A19250  705 GAuAccAuAuuucGGGccATsT A19251  706 UGGCCCGAAAuAUGGuAUCTsT AD- 11927 1956-1974 GP A20158  707 cGGAcuGcuGuAucGAAccTsT A20159  708 GGUUCGAuAcAGcAGUCCGTsT AD- 12482 2107-2125 GP A20160  709 uGGAGuuAcAGGcGuuAuATsT A20161  710 uAuAACGCCUGuAACUCcATsT AD- 12483 2124-2142 GP A20162  711 uAAuuGcAGuuAucGcuuuTsT A20163  712 AAAGCGAuAACUGcAAUuATsT AD- 12484 2109-2127 GP A20164  713 GAGuuAcAGGcGuuAuAAuTsT A20165  714 AUuAuAACGCCUGuAACUCTsT AD- 12485 1958-1976 GP A20166  715 GAcuGcuGuAucGAAccAcTsT A20167  716 GUGGUUCGAuAcAGcAGUCTsT AD- 12486 1890-1908 GP A20168  717 uccucAAccGuAAGGcAAuTsT A20169  718 AUUGCCUuACGGUUGAGGATsT AD- 12487 1891-1909 GP A20170  719 ccucAAccGuAAGGcAAuuTsT A20171  720 AAUUGCCUuACGGUUGAGGTsT AD- 12488 1307-1325 GP A20172  721 AAuAcAcccGuGuAuAAAcTsT A20173  722 GUUuAuAcACGGGUGuAUUTsT AD- 12489 1823-1841 GP A20174  723 GccAAcGAGAcGAcucAAGTsT A20175  724 CUUGAGUCGUCUCGUUGGCTsT AD- 12490 2110-2128 GP A20176  725 AGuuAcAGGcGuuAuAAuuTsT A20177  726 AAUuAuAACGCCUGuAACUTsT AD- 12491 1308-1326 GP A20178  727 AuAcAcccGuGuAuAAAcuTsT A20179  728 AGUUuAuAcACGGGUGuAUTsT AD- 12492 2113-2131 GP A20180  729 uAcAGGcGuuAuAAuuGcATsT A20181  730 UGcAAUuAuAACGCCUGuATsT AD- 12493 1654-1672 GP A20182  731 cAAuGcucAAcccAAAuGcTsT A20183  732 GcAUUUGGGUUGAGcAUUGTsT AD- 12494 1824-1842 GP A20184  733 ccAAcGAGAcGAcucAAGcTsT A20185  734 GCUUGAGUCGUCUCGUUGGTsT AD- 12495 1313-1331 GP A20186  735 cccGuGuAuAAAcuuGAcATsT A20187  736 UGUcAAGUUuAuAcACGGGTsT AD- 12496 1873-1891 GP A20188  737 GcuAcGcAccuuuucAAucTsT A20189  738 GAUUGAAAAGGUGCGuAGCTsT AD- 12497 1953-1971 GP A20190  739 GAccGGAcuGcuGuAucGATsT A20191  740 UCGAuAcAGcAGUCCGGUCTsT AD- 12498 1964-1982 GP A20192  741 uGuAucGAAccAcAuGAuuTsT A20193  742 AAUcAUGUGGUUCGAuAcATsT AD- 12499 329-347 VP30 A20194  743 AGGuGAGuAccGucAAucATsT A20195  744 UGAUUGACGGuACUcACCUTsT AD- 12500 426-444 VP30 A20196  745 AAAGAcAuAuGuccGAccuTsT A20197  746 AGGUCGGAcAuAUGUCUUUTsT AD- 12501 842-860 VP30 A20198  747 ucucGAAGuAuAucAAcGATsT A20199  748 UCGUUGAuAuACUUCGAGATsT AD- 12502 909-927 VP30 A20200  749 uGGGAccGAcAAucccuAATsT A20201  750 UuAGGGAUUGUCGGUCCcATsT AD- 12503 523-541 VP30 A20202  751 uccuAcuAAucGcccGuAATsT A20203  752 UuACGGGCGAUuAGuAGGATsT AD- 12504 429-447 VP30 A20204  753 GAcAuAuGuccGAccuuGATsT A20205  754 UcAAGGUCGGAcAuAUGUCTsT AD- 12505 521-539 VP30 A20206  755 AcuccuAcuAAucGcccGuTsT A20207  756 ACGGGCGAUuAGuAGGAGUTsT AD- 12506 903-921 VP30 A20208  757 cAAcAAuGGGAccGAcAAuTsT A20209  758 AUUGUCGGUCCcAUUGUUGTsT AD- 12507 355-373 VP30 A20210  759 ccucAcAAGuGcGcGuuccTsT A20211  760 GGAACGCGcACUUGUGAGGTsT AD- 12508 337-355 VP30 A20212  761 AccGucAAucAAGGAGcGcTsT A20213  762 GCGCUCCUUGAUUGACGGUTsT AD- 12509 908-926 VP24 A19262  763 cuGucGuuGAuucGAuccATsT A19263  764 UGGAUCGAAUcAACGAcAGTsT AD- 11933 522-540 VP24 A19272  765 uuGucuuAAGcGAccucuGTsT A19273  766 cAGAGGUCGCUuAAGAcAATsT AD- 11938 790-808 VP24 A19274  767 uuuGAuuGAAcccuuAGcATsT A19275  768 UGCuAAGGGUUcAAUcAAATsT AD- 11939 863-881 VP24 A20214  769 AAcAuGcGAAcAcAAcGuGTsT A20215  770 cACGUUGUGUUCGcAUGUUTsT AD- 12510 1102-1120 VP24 A20216  771 uGGGccGGcGAAAuuuuccTsT A20217  772 GGAAAAUUUCGCCGGCCcATsT AD- 12511 912-930 VP24 A20218  773 cGuuGAuucGAuccAAuAuTsT A20219  774 AuAUUGGAUCGAAUcAACGTsT AD- 12512 954-972 VP24 A20220  775 AuGcucuAcAuGucGuGAATsT A20221  776 UUcACGAcAUGuAGAGcAUTsT AD- 12513 475-493 VP24 A20222  777 GGGAcGAuAcAAucuAAuATsT A20223  778 uAUuAGAUUGuAUCGUCCCTsT AD- 12514 1069-1087 VP24 A20224  779 AcccGAcAAAucGGcAAuGTsT A20225  780 cAUUGCCGAUUUGUCGGGUTsT AD- 12515 486-504 VP24 A20226  781 AucuAAuAucGcccAAAAATsT A20227  782 UUUUUGGGCGAuAUuAGAUTsT AD- 12516 525-543 VP24 A20228  783 ucuuAAGcGAccucuGuAATsT A20229  784 UuAcAGAGGUCGCUuAAGATsT AD- 12517 867-885 VP24 A20230  785 uGcGAAcAcAAcGuGucAATsT A20231  786 UUGAcACGUUGUGUUCGcATsT AD- 12518 1028-1046 VP24 A20232  787 AuAAcucGAAcuAAcAuGGTsT A20233  788 CcAUGUuAGUUCGAGUuAUTsT AD- 12519 471-489 VP24 A20234  789 cuAcGGGAcGAuAcAAucuTsT A20235  790 AGAUUGuAUCGUCCCGuAGTsT AD- 12520 1029-1047 VP24 A20236  791 uAAcucGAAcuAAcAuGGGTsT A20237  792 CCcAUGUuAGUUCGAGUuATsT AD- 12521 1948-1966 L A20238  793 cAGuuAGAGGGAGuAGcuuTsT A20239  794 AAGCuACUCCCUCuAACUGTsT AD- 12522 2003-2021 L A20240  795 AuAuGAGuuuAcAGcAccuTsT A20241  796 AGGUGCUGuAAACUcAuAUTsT AD- 12523 2005-2023 L A20242  797 AuGAGuuuAcAGcAccuuuTsT A20243  798 AAAGGUGCUGuAAACUcAUTsT AD- 12524 2070-2088 L A20244  799 uGGAuGcAuuAuAcAAuccTsT A20245  800 GGAUUGuAuAAUGcAUCcATsT AD- 12525 1959-1977 NP A19278  801 AccuuGGAcGGAGcGAAAATsT A19279  802 UUUUCGCUCCGUCcAAGGUTsT AD- 11941 1687-1705 NP A19280  803 cAuuucccGGGccGAucuATsT A19281  804 uAGAUCGGCCCGGGAAAUGTsT AD- 11942 1775-1793 NP A19282  805 uGuuGuuGAcccGuAuGAuTsT A19283  806 AUcAuACGGGUcAAcAAcATsT AD- 11943 384-402 NP A19284  807 GuuuAccuGAGAGccuAcATsT A19285  808 UGuAGGCUCUcAGGuAAACTsT AD- 11944 400-418 NP A19286  809 AcAAcAuGGAuAAAcGGGuTsT A19287  810 ACCCGUUuAUCcAUGUUGUTsT AD- 11945 1773-1791 NP A19288  811 GGuGuuGuuGAcccGuAuGTsT A19289  812 cAuACGGGUcAAcAAcACCTsT AD- 11946 1964-1982 NP A19290  813 GGAcGGAGcGAAAAAGGuGTsT A19291  814 cACCUUUUUCGCUCCGUCCTsT AD- 11947 411-429 NP A19292  815 AAAcGGGuGAGAGGuucAuTsT A19293  816 AUGAACCUCUcACCCGUUUTsT AD- 11948 1815-1833 NP A19294  817 GAcuAcGAGGAuucGGcuGTsT A19295  818 cAGCCGAAUCCUCGuAGUCTsT AD- 11949 407-425 NP A19296  819 GGAuAAAcGGGuGAGAGGuTsT A19297  820 ACCUCUcACCCGUUuAUCCTsT AD- 11950 2405-2423 NP A19298  821 uuAucAccuAAuGAGuGAuTsT A19299  822 AUcACUcAUuAGGUGAuAATsT AD- 11951 409-427 NP A19300  823 AuAAAcGGGuGAGAGGuucTsT A19301  824 GAACCUCUcACCCGUUuAUTsT AD- 11952 1811-1829 NP A19302  825 uccuGAcuAcGAGGAuucGTsT A19303  826 CGAAUCCUCGuAGUcAGGATsT AD- 11953 408-426 NP A19304  827 GAuAAAcGGGuGAGAGGuuTsT A19305  828 AACCUCUcACCCGUUuAUCTsT AD- 11954 1958-1976 NP A19306  829 GAccuuGGAcGGAGcGAAATsT A19307  830 UUUCGCUCCGUCcAAGGUCTsT AD- 11955 1973-1991 NP A19308  831 GAAAAAGGuGccGGAGuuGTsT A19309  832 cAACUCCGGcACCUUUUUCTsT AD- 11956 1810-1828 NP A19310  833 AuccuGAcuAcGAGGAuucTsT A19311  834 GAAUCCUCGuAGUcAGGAUTsT AD- 11957 1953-1971 NP A19312  835 GAuccGAccuuGGAcGGAGTsT A19313  836 CUCCGUCcAAGGUCGGAUCTsT AD- 11958 1692-1710 NP A19314  837 cccGGGccGAucuAuGAuGTsT A19315  838 cAUcAuAGAUCGGCCCGGGTsT AD- 11959 197-215 VP35 A19316  839 AccGGcAAAAuAccGcuAATsT A19317  840 UuAGCGGuAUUUUGCCGGUTsT AD- 11960 196-214 VP35 A19318  841 GAccGGcAAAAuAccGcuATsT A19319  842 uAGCGGuAUUUUGCCGGUCTsT AD- 11961 409-427 VP35 A19320  843 AucAcuAGAAGGucGAGuATsT A19321  844 uACUCGACCUUCuAGUGAUTsT AD- 11962 476-494 VP35 A19322  845 AuAucAucccuGAAucGcATsT A19323  846 UGCGAUUcAGGGAUGAuAUTsT AD- 11963 611-629 VP35 A19324  847 ccAucAuuGuAcGAGGAuGTsT A19325  848 cAUCCUCGuAcAAUGAUGGTsT AD- 11964 645-663 VP35 A19326  849 AAuuGAAAGAuccGAAcGGTsT A19327  850 CCGUUCGGAUCUUUcAAUUTsT AD- 11965 726-744 VP35 A19328  851 AGGAAAAuuucGGGcGAccTsT A19329  852 GGUCGCCCGAAAuuuUCCUTsT AD- 11966 1130-1148 VP35 A19330  853 GuAAGcucAuuuuGcGAuGTsT A19331  854 cAUCGcAAAAUGAGCUuACTsT AD- 11967 729-747 VP35 A19332  855 AAAAuuucGGGcGAccuuATsT A19333  856 uAAGGUCGCCCGAAAUUUUTsT AD- 11968 606-624 VP35 A19334  857 cAGGcccAucAuuGuAcGATsT A19335  858 UCGuAcAAUGAUGGGCCUGTsT AD- 11969 256-274 VP35 A19336  859 cccGAuAAccAuuAuuAGuTsT A19337  860 ACuAAuAAUGGUuAUCGGGTsT AD- 11970 478-496 VP35 A19338  861 AucAucccuGAAucGcAGcTsT A19339  862 GCUGCGAUUcAGGGAUGAUTsT AD- 11971 724-742 VP35 A19340  863 uGAGGAAAAuuucGGGcGATsT A19341  864 UCGCCCGAAAUUUUCCUcATsT AD- 11972 644-662 VP35 A19342  865 AAAuuGAAAGAuccGAAcGTsT A19343  866 CGUUCGGAUCUUUcAAUUUTsT AD- 11973 1239-1257 VP35 A19344  867 AuccuAAucAAuuGAuAAuTsT A19345  868 AUuAUcAAUUGAUuAGGAUTsT AD- 11974 1052-1070 VP35 A19346  869 AucGAuAGAGGuuGGGucuTsT A19347  870 AGACCcAACCUCuAUCGAUTsT AD- 11975 429-447 VP40 A19348  871 GcAAuuAuGcucGcAucuuTsT A19349  872 AAGAUGCGAGcAuAAUUGCTsT AD- 11976 1189-1207 VP40 A19350  873 AAAAuGuAcuAAucGGGucTsT A19351  874 GACCCGAUuAGuAcAUUUUTsT AD- 11977 1190-1208 VP40 A19352  875 AAAuGuAcuAAucGGGucATsT A19353  876 UGACCCGAUuAGuAcAUUUTsT AD- 11978 373-391 VP40 A19354  877 GGuuGccAcucGGAAuuGcTsT A19355  878 GcAAUUCCGAGUGGcAACCTsT AD- 11979 439-457 VP40 A19356  879 ucGcAucuuAuAcGAucAcTsT A19357  880 GUGAUCGuAuAAGAUGCGATsT AD- 11980 441-459 VP40 A19358  881 GcAucuuAuAcGAucAcccTsT A19359  882 GGGUGAUCGuAuAAGAUGCTsT AD- 11981 1121-1139 VP40 A19360  883 AuAGcAAcucAAucGAcuuTsT A19361  884 AAGUCGAUUGAGUUGCuAUTsT AD- 11982 1127-1145 VP40 A19362  885 AcucAAucGAcuuuuAGGATsT A19363  886 UCCuAAAAGUCGAUUGAGUTsT AD- 11983 1193-1211 VP40 A19364  887 uGuAcuAAucGGGucAAGGTsT A19365  888 CCUUGACCCGAUuAGuAcATsT AD- 11984 1298-1316 VP40 A19366  889 AcAuGcAuAAGcGAuccAuTsT A19367  890 AUGGAUCGCUuAUGcAUGUTsT AD- 11985 1307-1325 VP40 A19368  891 AGcGAuccAuAcuucGcccTsT A19369  892 GGGCGAAGuAUGGAUCGCUTsT AD- 11986 361-379 VP40 A19370  893 AAAucccuAuuuGGuuGccTsT A19371  894 GGcAACcAAAuAGGGAUUUTsT AD- 11987 437-455 VP40 A19372  895 GcucGcAucuuAuAcGAucTsT A19373  896 GAUCGuAuAAGAUGCGAGCTsT AD- 11988 857-875 VP40 A19374  897 GAGuAucAuuGGGAucGAGTsT A19375  898 CUCGAUCCcAAUGAuACUCTsT AD- 11989 484-502 VP40 A19376  899 ucGuuAGAGuGAAucGAcuTsT A19377  900 AGUCGAUUcACUCuAACGATsT AD- 11990 1845-1863 GP A19378  901 GGAGcuGcGGAcAuAuAccTsT A19379  902 GGuAuAUGUCCGcAGCUCCTsT AD- 11991 254-272 GP A19380  903 GAGAuuGAccAGcuAGucuTsT A19381  904 AGACuAGCUGGUcAAUCUCTsT AD- 11992 461-479 GP A19382  905 ccGGAcGGGAGcGAAuGcuTsT A19383  906 AGcAUUCGCUCCCGUCCGGTsT AD- 11993 466-484 GP A19384  907 cGGGAGcGAAuGcuuAcccTsT A19385  908 GGGuAAGcAUUCGCUCCCGTsT AD- 11994 933-951 GP A19386  909 uAAuuuGGAcAcuAGAuGcTsT A19387  910 GcAUCuAGUGUCcAAAUuATsT AD- 11995 1045-1063 GP A19388  911 uuAucGcucAAcGAGAcAGTsT A19389  912 CUGUCUCGUUGAGCGAuAATsT AD- 11996 1100-1118 GP A19390  913 GAAGAAucuccGAccGGGcTsT A19391  914 GCCCGGUCGGAGAuUCuUCTsT AD- 11997 1102-1120 GP A19392  915 AGAAucuccGAccGGGccATsT A19393  916 UGGCCCGGUCGGAGAUUCUTsT AD- 11998 1191-1209 GP A19394  917 AAcAAcAuuGccGucucAGTsT A19395  918 CUGAGACGGcAAUGUUGUUTsT AD- 11999 1203-1221 GP A19396  919 GucucAGAAuucGAcAGAATsT A19397  920 uUCuGUCGAAuUCuGAGACTsT AD- 12000 1844-1862 GP A19398  921 cGGAGcuGcGGAcAuAuAcTsT A19399  922 GuAuAUGUCCGcAGCUCCGTsT AD- 12001 255-273 GP A19400  923 AGAuuGAccAGcuAGucuGTsT A19401  924 cAGACuAGCUGGUcAAUCUTsT AD- 12002 1212-1230 GP A19402  925 uucGAcAGAAGGucGAAGATsT A19403  926 UCUUCGACCUUCUGUCGAATsT AD- 12003 1706-1724 GP A19404  927 GGAucccGuAcuuuGGAccTsT A19405  928 GGUCcAAAGuACGGGAUCCTsT AD- 12004 125-143 GP A19406  929 cuuAGccuAcuccAAuuGcTsT A19407  930 GcAAUUGGAGuAGGCuAAGTsT AD- 12005 264-282 GP A19408  931 AGcuAGucuGcAAGGAucATsT A19409  932 UGAUCCUUGcAGACuAGCUTsT AD- 12006 332-350 GP A19410  933 AGcGGAGuAucuAcuGAuATsT A19411  934 uAUcAGuAGAuACUCCGCUTsT AD- 12007 464-482 GP A19412  935 GAcGGGAGcGAAuGcuuAcTsT A19413  936 GuAAGcAUUCGCUCCCGUCTsT AD- 12008 1210-1228 GP A19414  937 AAuucGAcAGAAGGucGAATsT A19415  938 uUCGACCuUCuGUCGAAUUTsT AD- 12009 1213-1231 GP A19416  939 ucGAcAGAAGGucGAAGAGTsT A19417  940 CUCuUCGACCuUCuGUCGATsT AD- 12010 1850-1868 GP A19418  941 uGcGGAcAuAuAccAuAcuTsT A19419  942 AGuAUGGuAuAUGUCCGcATsT AD- 12011 124-142 GP A19420  943 ucuuAGccuAcuccAAuuGTsT A19421  944 cAAUUGGAGuAGGCuAAGATsT AD- 12012 1044-1062 GP A19422  945 uuuAucGcucAAcGAGAcATsT A19423  946 UGUCUCGUUGAGCGAuAAATsT AD- 12013 265-283 GP A19424  947 GcuAGucuGcAAGGAucAuTsT A19425  948 AUGAUCCUUGcAGACuAGCTsT AD- 12014 361-379 VP30 A19426  949 uAGAGucccuAcGGuuuucTsT A19427  950 GAAAACCGuAGGGACUCuATsT AD- 12015 324-342 VP30 A19428  951 cAAcAGAcuAccGuAGuAGTsT A19429  952 CuACuACGGuAGUCUGUUGTsT AD- 12016  994-1012 VP30 A19430  953 AGGccuAcGcuuAcuuGccTsT A19431  954 GGcAAGuAAGCGuAGGCCUTsT AD- 12017 248-266 VP30 A19432  955 AGGAAuucAcGuGccGAccTsT A19433  956 GGUCGGcACGUGAAUUCCUTsT AD- 12018 491-509 VP30 A19434  957 cuuGAAAGccuAAccGAccTsT A19435  958 GGUCGGUuAGGCUUUcAAGTsT AD- 12019 322-340 VP30 A19436  959 AAcAAcAGAcuAccGuAGuTsT A19437  960 ACuACGGuAGUCUGUUGUUTsT AD- 12020 323-341 VP30 A19438  961 AcAAcAGAcuAccGuAGuATsT A19439  962 uACuACGGuAGUCUGUUGUTsT AD- 12021 517-535 VP30 A19440  963 ccuAcuucuuAuAGcAcGGTsT A19441  964 CCGUGCuAuAAGAAGuAGGTsT AD- 12022 295-313 VP30 A19442  965 GAcAAGAuccAuuucccGGTsT A19443  966 CCGGGAAAuGGAUCuuGUCTsT AD- 12023 229-247 VP30 A19444  967 ucGuGAGcGcGGGAGAucATsT A19445  968 UGAUCUCCCGCGCUcACGATsT AD- 12024 251-269 VP30 A19446  969 AAuucAcGuGccGAccAGcTsT A19447  970 GCUGGUCGGcACGUGAAUUTsT AD- 12025 340-358 VP30 A19448  971 uAGucGAAGuAcuucGcAATsT A19449  972 UUGCGAAGuACUUCGACuATsT AD- 12026 1350-1368 VP30 A19450  973 ucccuAGAAGcGuuGAAucTsT A19451  974 GAUUcAACGCUUCuAGGGATsT AD- 12027 1057-1075 VP24 A19452  975 uAuGGGuuAucuuGucGAGTsT A19453  976 CUCGAcAAGAuAACCcAuATsT AD- 12028 878-896 VP24 A19454  977 AAcAuGAGAAcucAAcGAGTsT A19455  978 CUCGUUGAGUUCUcAUGUUTsT AD- 12029 1056-1074 VP24 A19456  979 AuAuGGGuuAucuuGucGATsT A19457  980 UCGAcAAGAuAACCcAuAUTsT AD- 12030 1137-1155 VP24 A19458  981 uAcuAcAuGAAucGAcAcuTsT A19459  982 AGUGUCGAUUcAUGuAGuATsT AD- 12031 1099-1117 VP24 A19460  983 GAuGGAuAuAcGAcAcccuTsT A19461  984 AGGGUGUCGuAuAUCcAUCTsT AD- 12032 1591-1609 VP24 A19462  985 AGcccAAAuuAAcAcGGuATsT A19463  986 uACCGUGUuAAUUUGGGCUTsT AD- 12033 1094-1112 VP24 A19464  987 ucuGcGAuGGAuAuAcGAcTsT A19465  988 GUCGuAuAUCcAUCGcAGATsT AD- 12034 1135-1153 VP24 A19466  989 cuuAcuAcAuGAAucGAcATsT A19467  990 UGUCGAUUcAUGuAGuAAGTsT AD- 12035 152-170 VP24 A19468  991 cuAGGcuAGGGuuuAuAGuTsT A19469  992 ACuAuAAACCCuAGCCuAGTsT AD- 12036 624-642 VP24 A19470  993 AccAAAAGGGuAuuAcccuTsT A19471  994 AGGGuAAuACCCUUUUGGUTsT AD- 12037

TABLE 3 Ebola Ebola Ebola Zaire GFP assay Zaire plaque Ebola Sudan IF assay Sudan plaque duplex % reduction % reduction vs % reduction % reduction vs name 100 nM 10 nM 1 nM no siRNA 100 nM 10 nM 1 nM no siRNA AD-11542 90.7 80.1 55.2 55.24 −5.3 −1.5 −11.8 −103.39 AD-11543 62.7 55.9 47.8 55.83 −11.9 10.2 −9.0 −7.12 AD-11544 63.5 32.8 41.0 42.06 22.5 34.6 61.1 −16.95 AD-11545 73.0 71.8 61.4 47.23 61.5 71.9 71.8 39.41 AD-11546 94.5 88.3 72.5 86.12 −8.8 −73.8 5.5 55.93 AD-11547 79.8 62.8 48.6 36.44 −20.7 15.8 −4.0 18.64 AD-11548 −15.4 −13.0 −15.6 19.3 29.2 49.3 AD-11549 3.8 13.8 16.1 44.12 63.7 51.5 90.4 94.38 AD-11550 17.5 −1.2 −10.5 −41.1 −39.8 −29.4 AD-11551 −14.2 −20.4 −21.3 −32.6 −23.9 −30.6 AD-11552 −14.7 −11.9 −6.5 −22.7 −9.5 11.9 AD-11553 4.7 7.4 13.9 27.67 44.5 40.9 44.6 80.33 AD-11554 −12.6 −20.5 −32.1 −12.6 −17.7 −8.0 AD-11555 −20.8 −22.2 −36.7 −9.8 −8.9 0.8 AD-11556 6.4 −11.6 −21.7 29.03 11.1 37.1 34.7 −17.37 AD-11557 30.6 22.0 −8.7 −175.73 41.5 48.3 78.3 82.20 AD-11558 3.0 1.2 −33.7 72.97 −23.5 −18.2 −30.8 82.49 AD-11559 −29.1 −38.0 −42.9 −2.4 −37.3 −26.5 AD-11560 −42.0 −46.1 −54.6 19.8 0.7 19.1 AD-11561 −16.4 −16.6 −15.9 37.38 50.5 61.2 57.4 −129.83 AD-11562 12.0 −13.9 −63.1 61.33 −35.3 −46.2 −42.4 63.56 AD-11563 −45.3 −51.6 −61.7 −45.3 −54.7 −42.9 AD-11564 −19.0 −31.3 −44.0 −38.5 −32.3 −0.1 AD-11565 −27.0 −4.4 −10.7 50.32 6.7 47.4 52.9 26.95 AD-11566 6.8 6.0 −0.5 32.0 18.2 0.7 AD-11567 −1.1 −5.7 0.3 3.1 −4.6 14.4 AD-11568 10.3 7.9 11.4 −0.7 27.6 25.6 AD-11569 17.6 22.0 15.4 33.01 47.1 51.3 63.7 −85.01 AD-11570 23.8 5.9 −15.4 98.14 9.3 −5.5 −15.3 −217.80 AD-11571 −27.5 −23.9 −32.4 −8.5 −13.0 10.8 AD-11572 −35.2 −25.7 −26.1 4.3 8.8 18.6 AD-11573 −8.3 16.7 15.7 46.60 55.9 76.5 37.8 −22.05 AD-11574 1.1 −12.0 −27.6 12.5 −2.9 −11.3 AD-11575 −29.9 −30.0 −35.9 1.6 27.3 −11.4 AD-11576 −9.4 −8.2 −20.8 0.1 34.6 3.1 AD-11577 −8.5 −0.1 13.7 45.2 31.5 23.2 AD-11578 9.8 17.0 4.1 −40.1 −56.3 −53.3 AD-11579 15.1 12.2 −7.8 −47.6 −37.3 −18.5 AD-11580 −4.4 2.3 4.1 76.38 14.2 4.9 33.6 12.97 AD-11581 10.6 2.5 3.4 −26.97 57.4 65.1 81.7 −109.94 AD-11582 10.6 4.3 −33.2 −1.17 −99.7 −93.3 −90.8 −533.33 AD-11583 −16.6 −18.4 −28.3 −85.8 −72.4 −55.3 AD-11584 −24.1 −12.0 −18.7 59.87 −1.0 54.0 16.5 1.61 AD-11585 −7.2 −9.6 9.1 51.46 37.5 19.1 45.7 82.71 AD-11586 −6.8 −0.7 −9.1 −81.1 −87.9 −86.9 AD-11587 6.1 −0.4 0.9 −80.7 −6.2 −51.8 AD-11588 20.9 10.4 −9.5 99.40 −12.9 −0.1 20.5 −117.23 AD-11589 28.7 24.3 16.1 35.75 18.2 38.7 54.2 88.14 AD-11590 20.7 28.8 3.0 98.81 −38.5 −55.2 20.9 44.92 AD-11591 −18.3 −29.6 −27.0 −3.1 −40.1 −30.1 AD-11592 −11.3 −14.7 −12.3 −36.3 −38.7 −46.1 AD-11593 3.8 5.0 −12.3 1.8 −15.8 4.6 AD-11594 33.4 4.9 −3.2 99.07 −25.2 −31.3 −21.7 7.63 AD-11595 −30.9 −37.7 −54.2 −11.6 −2.7 −2.7 AD-11596 −8.2 −14.8 −3.3 −7.8 26.8 3.5 AD-11597 13.0 13.0 11.7 21.7 28.2 25.2 83.00 AD-11598 40.0 −1.6 −10.4 98.91 −30.2 −33.7 −17.7 0.00 AD-11599 13.0 24.6 −18.3 98.79 −20.9 −22.8 −50.8 34.32 AD-11600 16.7 2.8 −8.1 98.52 −4.3 −28.5 6.8 −120.34 AD-11601 10.4 25.3 2.0 71.20 23.0 6.3 7.9 −652.16 AD-11602 39.7 45.0 24.4 38.73 47.4 37.7 54.8 48.13 AD-11603 41.2 42.4 36.0 54.85 38.2 35.7 43.8 73.04 AD-11604 39.6 36.3 31.6 −1.51 37.0 56.6 52.8 84.65 AD-11605 50.2 38.8 21.2 60.19 48.1 58.6 77.6 66.95 AD-11606 41.5 36.8 1.4 89.23 53.2 33.2 37.0 79.32 AD-11607 −12.8 2.7 −9.9 38.83 29.0 8.3 21.4 −13.98 AD-11608 10.9 −6.7 6.1 14.24 39.5 49.3 42.9 −75.07 AD-11609 27.3 32.9 29.0 51.46 36.8 40.7 50.2 20.81 AD-11610 23.9 19.7 16.0 23.95 37.7 70.3 49.6 97.93 AD-11611 5.6 11.9 16.1 30.7 8.5 15.6 AD-11612 −2.9 −4.0 −14.4 9.9 21.9 10.0 AD-11613 13.4 32.7 23.7 −2.6 17.5 44.4 AD-11614 9.0 14.3 10.3 21.9 9.9 −29.6 AD-11615 −5.9 22.3 −0.9 −24.8 −16.9 −21.2 AD-11616 2.3 5.5 11.0 −10.4 −7.6 26.4 AD-11617 14.3 5.3 −1.9 −617.15 39.8 62.5 91.5 14.55 AD-11618 −2.5 −4.3 −1.2 −11.0 −26.8 −28.6 AD-11619 −8.3 −37.8 −30.2 −33.9 −43.8 −23.9 AD-11620 11.0 −19.2 −37.5 −30.5 −12.0 0.7 AD-11621 −29.1 −4.5 4.7 −255.66 60.9 64.7 78.8 74.06 AD-11622 11.9 15.0 4.2 9.8 −29.1 −15.8 AD-11623 7.7 −17.8 −24.6 −27.3 −48.1 −19.4 AD-11624 −16.3 −36.6 −45.8 −36.1 −17.2 −8.3 AD-11625 45.0 11.0 0.3 37.98 19.5 48.2 43.1 −23.73 AD-11626 −3.6 13.2 11.9 −25.4 −81.4 −80.3 AD-11627 34.1 24.7 21.1 48.69 −46.8 −73.0 −54.8 12.71 AD-11628 −8.9 −1.4 −13.8 9.60 −9.5 6.1 35.2 59.80 AD-11629 22.9 23.0 11.8 −73.11 65.3 71.2 75.1 3.39 AD-11630 12.2 19.0 −2.0 −99.9 −123.8 −85.0 AD-11631 −10.4 −15.2 −18.3 −127.0 −87.2 −59.2 AD-11632 −50.7 −49.9 −49.4 −128.91 −32.4 1.3 29.8 51.76 AD-11633 −39.4 −10.2 1.8 −19.31 20.6 42.9 57.4 49.57 AD-11634 2.2 12.3 −14.1 −55.8 −129.3 −136.9 AD-11635 −44.3 −46.0 −29.5 −60.2 −89.0 −66.2 AD-11636 −48.8 −44.7 −41.1 −35.4 −17.4 7.3 AD-11637 −36.8 −27.2 −17.3 59.55 34.3 33.8 52.8 80.40 AD-11638 −8.4 8.5 −3.9 −9.4 12.4 28.9 AD-11639 −47.6 −1.7 36.0 23.31 2.9 20.2 12.6 −97.46 AD-11640 69.4 39.4 34.6 75.14 66.0 71.5 82.5 49.15 AD-11641 42.6 15.2 15.9 65.14 73.1 81.9 87.7 96.50 AD-11642 24.8 21.4 32.7 −42.93 89.8 87.4 87.4 4.03 AD-11643 37.7 53.8 52.7 89.14 94.3 94.2 97.5 −22.03 AD-11644 54.1 17.7 5.5 94.29 26.7 38.5 51.2 31.78 AD-11645 5.9 2.5 −2.5 51.97 64.7 68.1 80.1 93.34 AD-11646 −1.7 2.1 7.9 59.55 72.6 76.8 79.0 92.72 AD-11647 8.4 8.8 37.5 57.28 75.6 81.7 93.7 74.71 AD-11648 56.9 19.2 8.1 66.10 −15.4 −9.9 13.0 71.19 AD-11649 −3.3 −6.9 −3.5 65.47 36.0 54.2 64.9 82.84 AD-11650 1.9 −2.5 −1.5 17.28 58.7 65.3 59.6 2.31 AD-11651 6.7 9.4 30.9 65.70 70.3 87.1 91.2 83.96 AD-11652 55.8 27.7 10.3 −56.8 59.6 68.4 33.90 AD-11653 12.4 13.8 10.9 86.84 66.4 70.4 75.8 2.02 AD-11654 13.8 7.2 10.7 76.1 73.8 73.8 −123.92 AD-11655 9.1 14.6 40.5 −7.01 82.4 83.9 92.6 −146.11 AD-11656 39.1 9.6 −1.0 81.71 −21.9 30.7 19.0 20.34 AD-11657 −1.1 1.1 0.2 −3.1 20.7 48.9 AD-11658 7.3 0.9 1.5 86.84 55.5 50.8 41.3 93.52 AD-11659 2.9 4.1 28.0 78.79 46.4 51.1 66.6 79.47 AD-11660 23.8 13.0 0.9 80.57 11.0 20.8 −57.0 90.51 AD-11661 −6.4 −8.0 −6.1 −37.1 −16.9 19.1 AD-11662 −1.6 −7.9 −7.9 10.9 10.7 27.7 AD-11663 1.6 5.6 28.1 25.4 20.4 30.8 AD-11664 11.9 7.6 3.9 50.16 54.4 63.1 66.8 77.95 AD-11665 5.1 1.2 0.2 15.10 52.7 65.2 62.3 −13.26 AD-11666 0.0 −3.5 5.3 5.72 67.9 80.3 80.3 79.54 AD-11667 3.7 2.9 8.0 47.73 83.6 80.4 90.6 84.70 AD-11668 16.3 −0.3 −1.3 −91.6 −4.4 2.8 AD-11669 −1.0 3.8 0.3 3.4 33.5 43.3 AD-11670 −0.1 −4.6 −2.6 35.28 42.7 43.6 62.6 −5.48 AD-11671 0.1 1.1 16.0 80.58 61.0 65.1 72.7 13.54 AD-11672 8.2 −0.1 −2.2 −69.9 25.3 −57.8 AD-11673 1.7 0.9 3.2 −46.1 −22.7 1.5 AD-11674 −4.2 −3.0 −6.0 34.4 14.8 32.2 AD-11675 −0.6 0.6 18.4 11.1 45.1 59.7 AD-11676 22.1 11.5 7.7 78.86 75.7 86.4 78.6 16.95 AD-11677 5.6 −3.1 3.2 86.1 78.0 87.1 1.27 AD-11678 −2.3 −7.8 5.0 87.06 86.4 86.6 86.6 −141.35 AD-11679 5.6 7.3 34.4 28.26 88.3 88.6 90.9 −79.25 AD-11680 30.4 7.9 −0.5 75.62 −38.9 13.4 −88.3 72.03 AD-11681 −3.7 −10.1 −0.2 14.4 25.0 24.2 AD-11682 −10.0 −11.0 −7.7 −39.9 53.8 57.2 AD-11683 −6.4 6.6 32.3 92.99 59.6 53.3 48.2 57.85 AD-11684 31.5 14.4 2.9 33.26 −156.0 −119.6 −198.2 87.80 AD-11685 0.0 −6.5 −9.5 −6.15 −43.0 −107.3 −93.7 −20.61 AD-11686 −12.0 −7.9 −4.7 88.12 −134.6 −69.2 −151.8 43.11 AD-11687 −4.8 6.3 29.0 −77.4 −41.4 −79.0 AD-11688 40.0 28.5 26.7 −15.66 73.4 79.8 88.0 66.95 AD-11689 34.4 27.1 32.4 57.33 83.4 74.8 86.5 85.59 AD-11690 24.0 30.2 42.1 71.71 82.5 89.4 89.4 83.05 AD-11691 47.9 44.1 55.3 87.43 92.0 93.9 97.0 70.96 AD-11694 44.3 8.5 5.7 2.1 4.8 13.6 AD-11695 1.5 0.5 −5.3 42.1 36.7 46.0 AD-11696 5.1 4.8 10.8 49.2 56.9 76.3 AD-11698 18.4 20.4 45.5 59.09 69.5 79.5 82.0 54.66 AD-11700 30.4 8.5 −2.1 84.00 −151.2 −108.0 −67.5 4.52 AD-11704 −7.2 −6.1 −9.9 −37.2 −56.5 −32.4 AD-11705 −2.9 −2.4 −4.7 −7.3 0.9 −14.8 AD-11706 8.5 21.1 99.9 21.5 −8.9 33.9 AD-11707 41.8 25.9 21.9 90.69 79.3 84.2 85.1 63.14 AD-11708 27.2 27.4 28.1 83.92 80.0 81.1 83.7 24.58 AD-11710 31.0 37.7 43.0 77.54 86.9 89.6 89.6 99.70 AD-11711 33.8 36.5 48.2 73.43 91.1 89.8 93.9 −34.75 AD-11712 81.1 20.2 8.0 79.71 22.6 −4.3 27.5 −13.56 AD-11713 −8.6 −4.0 −2.1 39.1 39.1 51.8 AD-11714 −8.7 −8.3 −4.3 63.27 45.0 66.1 74.5 39.48 AD-11715 0.8 14.9 40.7 −92.23 79.0 82.0 86.9 1.15 AD-11716 32.4 8.3 1.8 83.05 −46.0 −51.4 −11.3 −577.97 AD-11717 2.2 −0.5 −0.6 −1.5 −13.0 −14.3 AD-11718 −8.1 −11.9 −19.8 2.4 18.8 29.2 AD-11719 4.2 11.6 33.8 57.93 55.3 56.6 74.0 −2.02 AD-11720 29.8 17.3 10.4 77.05 86.4 91.8 95.6 −373.73 AD-11721 14.6 13.7 12.4 82.56 90.8 91.1 95.1 −31.70 AD-11722 17.0 15.1 23.7 82.96 94.1 91.7 91.7 −112.39 AD-11723 16.0 13.5 30.5 90.99 94.1 95.5 95.7 −55.62 AD-11724 33.9 10.4 5.1 99.98 63.2 73.2 73.7 −1.27 AD-11725 6.4 −2.0 0.0 93.62 85.5 92.4 89.5 −172.62 AD-11726 2.4 0.2 0.2 58.58 90.3 91.9 94.4 −2.54 AD-11727 −1.0 2.8 20.2 4.72 93.9 94.5 98.3 49.86 AD-11728 30.7 12.9 4.0 73.43 26.9 27.5 41.0 30.51 AD-11729 5.1 1.5 −4.3 26.86 51.9 65.4 58.9 −20.46 AD-11730 2.6 1.3 0.8 24.70 60.2 67.7 71.6 52.02 AD-11731 4.9 3.3 24.1 79.94 66.8 67.3 89.0 96.16 AD-11732 33.6 9.3 6.0 63.43 63.0 79.9 87.5 70.34 AD-11733 2.2 2.8 −0.7 75.57 84.2 89.7 85.1 −9.51 AD-11734 8.6 6.7 10.8 90.52 90.8 90.6 90.6 −119.16 AD-11735 6.9 9.3 31.4 −22.87 90.8 88.5 94.5 −77.23 AD-11736 31.5 9.9 3.0 21.14 29.9 39.5 45.3 −611.86 AD-11737 −8.0 −3.4 −1.7 −183.17 78.3 88.4 82.5 14.41 AD-11738 −0.2 1.5 −4.7 −102.05 85.3 86.4 80.4 10.52 AD-11739 7.4 3.8 21.5 52.75 53.8 55.2 83.5 89.27 AD-11740 30.0 11.7 −0.4 53.43 −87.3 −64.8 12.1 38.98 AD-11741 −3.5 −6.1 −2.9 42.39 27.2 47.7 36.1 −32.56 AD-11742 −1.0 −1.9 −6.0 40.35 49.9 56.9 20.5 12.25 AD-11743 0.1 6.6 26.9 37.35 46.3 24.7 71.2 26.08 AD-11744 40.5 24.2 21.0 75.24 42.9 52.0 90.3 32.20 AD-11745 26.3 23.1 23.3 55.43 64.3 74.1 84.5 54.24 AD-11746 7.2 0.9 −4.8 89.82 42.3 74.8 8.6 33.49 AD-11747 1.6 −3.5 −5.4 54.9 5.8 25.4 AD-11748 −4.3 0.5 0.9 30.3 10.9 10.9 AD-11749 8.4 3.9 1.0 41.4 −3.7 54.3 AD-11750 4.8 2.1 0.0 44.9 30.4 71.5 AD-11751 3.3 0.6 −2.2 34.3 −18.6 29.4 AD-11752 17.7 6.5 3.2 −27.63 19.8 19.6 −0.1 61.08 AD-11753 1.7 1.2 0.9 −62.5 −40.7 28.2 AD-11754 3.7 1.8 0.7 69.9 91.1 44.9 AD-11755 37.7 26.6 10.8 −58.93 10.1 0.6 28.8 47.05 AD-11756 −1.0 −0.6 0.3 −39.8 −16.7 −5.7 AD-11757 0.2 0.0 1.8 −46.4 −12.7 −2.7 AD-11758 18.9 11.7 7.5 21.83 27.3 12.4 −9.8 70.02 AD-11759 26.1 15.1 18.8 −595.93 −6.9 −3.8 −22.6 55.98 AD-11760 21.9 19.5 6.0 11.60 −61.2 6.6 6.6 22.49 AD-11761 18.1 8.6 6.4 −67.30 39.7 43.4 58.0 71.77 AD-11762 15.4 9.7 4.2 −335.24 38.7 −86.0 12.4 73.68 AD-11763 6.8 7.3 3.7 −3.6 −0.7 8.7 AD-11764 5.1 5.7 0.9 −34.9 28.7 18.2 AD-11765 14.8 8.0 4.3 5.98 32.1 27.3 58.4 76.08 AD-11766 2.9 3.5 3.9 13.4 −6.1 −68.1 AD-11767 24.1 15.1 5.5 7.18 32.9 −27.7 0.2 9.57 AD-11768 19.2 16.5 4.3 30.34 −92.5 −3.0 4.0 55.98 AD-11769 5.6 2.3 2.6 6.7 25.7 43.9 AD-11770 14.0 7.2 2.2 −16.41 19.1 34.2 35.3 49.60 AD-11771 2.8 2.1 1.3 37.7 19.1 15.6 AD-11772 4.0 2.2 2.6 70.0 52.3 52.3 AD-11773 1.3 −0.6 −0.7 52.0 65.8 65.4 AD-11774 2.0 1.5 0.5 73.1 −18.3 6.5 AD-11775 2.3 0.3 −0.2 57.8 49.1 5.5 AD-11776 2.7 0.4 1.6 59.6 48.4 41.0 AD-11777 3.6 1.3 0.0 10.4 47.2 53.8 AD-11778 0.9 −0.9 −0.8 40.4 −13.5 −17.7 AD-11779 6.3 1.7 −0.5 42.1 2.9 −6.9 AD-11780 5.8 0.1 0.1 29.5 −17.6 20.3 AD-11781 2.3 1.0 −0.2 8.8 33.5 39.1 AD-11782 −1.7 −4.0 −4.1 48.1 44.5 56.1 AD-11783 −3.5 −2.1 −1.5 34.8 16.7 44.2 AD-11784 5.7 3.7 −1.0 50.4 59.1 59.1 AD-11785 2.8 1.0 1.5 75.3 88.0 81.7 AD-11786 14.9 6.5 −2.9 97.46 −7.0 −34.8 −6.5 66.19 AD-11787 −0.3 0.0 −2.9 9.0 −8.6 18.2 AD-11788 −0.1 0.5 1.3 23.5 11.8 55.0 AD-11789 5.1 5.7 3.1 57.8 45.6 62.5 AD-11790 5.7 0.0 −4.0 18.8 −12.3 −1.9 AD-11791 −1.5 −2.6 −4.6 42.1 −27.4 10.4 AD-11792 −0.9 1.8 1.5 27.1 30.8 24.6 AD-11793 2.2 3.7 4.4 6.7 34.8 44.3 AD-11794 0.4 −0.5 −1.6 59.5 81.9 69.3 AD-11795 −1.9 −0.8 0.1 78.7 94.4 87.2 AD-11796 5.0 1.8 0.8 89.6 71.8 71.8 AD-11797 0.6 0.8 1.3 92.1 87.0 83.7 AD-11798 −0.2 −0.2 −1.8 67.4 69.7 45.4 AD-11799 −2.1 −1.9 −1.3 −49.1 −5.6 72.9 AD-11800 1.3 −1.0 −0.4 64.1 58.5 60.6 AD-11801 0.1 0.1 0.8 23.7 35.3 54.5 AD-11802 4.8 0.8 −0.4 −115.9 −81.0 −113.4 AD-11803 3.7 1.3 −2.1 10.5 22.6 16.3 AD-11804 −2.0 −1.1 0.0 16.0 19.8 36.1 AD-11805 −0.5 0.2 −0.4 −6.9 6.5 51.6 AD-11806 −11.1 −16.4 −13.0 79.5 70.3 29.3 AD-11807 13.3 −13.2 −11.2 −78.63 65.7 20.0 50.5 −58.37 AD-11808 −6.3 −9.0 9.4 27.5 30.6 30.6 AD-11809 −0.2 −11.7 −11.7 44.7 61.3 73.0 AD-11810 −15.2 −17.1 −17.8 80.1 81.6 81.7 AD-11811 −9.7 −12.1 −11.2 40.4 38.0 23.7 AD-11812 −8.1 −12.5 −15.0 21.4 12.4 22.7 AD-11813 29.3 −14.5 −6.8 −258.78 31.4 32.0 43.9 −423.13 AD-11814 −19.9 −18.8 −8.1 49.2 15.1 55.1 AD-11815 −12.8 −13.4 −14.9 62.5 29.3 36.0 AD-11816 −14.5 −15.2 −14.6 13.0 −11.9 46.2 AD-11817 −15.4 −15.2 −11.8 43.3 38.2 42.0 AD-11818 9.5 −1.9 −6.6 −176.59 69.0 43.6 35.2 39.23 AD-11819 −3.5 −1.4 −1.9 75.0 50.7 31.2 AD-11820 7.6 4.4 −2.0 −327.48 58.5 50.6 50.6 29.19 AD-11821 1.3 −0.5 1.6 42.4 26.4 49.4 AD-11822 7.7 −4.1 −4.2 82.6 70.2 71.9 AD-11823 −1.5 −2.3 −0.4 63.9 58.8 37.4 AD-11824 3.2 1.7 −2.7 33.5 13.3 37.3 AD-11825 0.1 −0.9 0.7 53.6 42.2 44.8 AD-11826 3.4 −6.1 −3.8 52.8 35.7 39.9 AD-11827 −4.2 −2.6 −1.1 54.5 26.3 15.2 AD-11828 0.8 −1.3 −1.4 9.3 −4.3 19.5 AD-11829 2.0 −1.6 1.1 32.2 16.0 32.0 AD-11830 −4.3 −7.5 −8.0 44.5 48.3 75.6 AD-11831 −6.4 −5.2 −4.1 39.3 56.5 67.3 AD-11832 −3.2 −2.5 −3.0 61.0 76.2 76.2 AD-11833 −1.4 −2.5 −1.2 80.6 87.2 91.0 AD-11834 18.8 2.8 −7.7 −260.69 7.3 −11.5 24.5 25.84 AD-11835 −2.0 −0.2 −4.6 52.7 59.4 61.0 AD-11836 3.3 0.7 −1.9 70.7 76.0 80.0 AD-11837 0.3 −2.3 −0.7 84.6 70.1 80.8 AD-11838 −7.4 −7.1 −8.8 −13.5 9.5 8.9 AD-11839 −5.6 −2.9 −2.2 −0.7 45.3 48.4 AD-11840 −1.7 1.3 −0.2 85.7 61.6 59.6 AD-11841 −3.8 −1.8 −2.3 60.7 52.5 50.8 AD-11842 14.4 7.7 0.8 35.57 −145.5 −117.2 −46.4 42.11 AD-11843 ND ND ND −68.1 −87.6 −36.1 AD-11844 0.0 1.4 −0.5 −72.1 −80.2 −80.2 AD-11845 3.9 2.0 1.1 −34.1 −60.1 −13.9 AD-11846 27.5 20.0 −7.1 25.19 −69.7 −62.0 −63.7 13.40 AD-11847 −5.9 −4.8 −6.2 −93.2 −61.3 −57.4 AD-11848 −1.3 0.6 −1.7 −89.3 −76.1 −18.3 AD-11849 −1.0 −1.4 50.6 −0.9 12.6 18.7 AD-11850 −4.1 2.9 −6.3 −15.1 −3.7 −34.5 AD-11851 −5.0 −4.6 −2.2 −13.3 −10.3 −15.2 AD-11852 −0.4 −0.6 −0.6 7.7 11.6 10.2 AD-11853 1.6 −0.6 −0.8 24.9 28.1 36.7 AD-11854 −0.6 −1.3 −1.8 50.9 35.6 21.2 AD-11855 5.0 3.4 1.6 47.8 24.7 28.6 AD-11856 2.3 0.9 −0.6 60.4 36.7 36.7 AD-11857 3.4 0.7 0.1 23.1 37.0 57.6 AD-11858 −2.3 −2.5 −2.7 59.8 78.3 41.7 AD-11859 0.6 2.0 −1.0 64.0 33.3 40.7 AD-11860 11.4 6.4 0.1 32.44 40.2 −5.8 34.3 54.70 AD-11861 3.2 1.7 −0.4 −6.3 −30.9 26.8 AD-11862 15.3 3.2 −3.1 −55.53 37.3 6.8 51.0 51.20 AD-11863 8.7 8.8 4.1 −77.56 26.0 17.7 37.8 80.86 AD-11864 8.9 3.5 −1.4 −179.90 40.7 27.9 −8.9 69.38 AD-11865 4.3 0.2 0.1 0.3 8.6 14.9 AD-11870 4.5 5.7 1.9 60.1 43.2 68.8 AD-11871 13.9 4.6 −0.4 86.72 59.8 62.3 72.1 AD-11872 12.4 9.9 −0.2 81.93 75.1 77.9 77.9 79.43 AD-11873 16.2 8.7 2.9 51.91 81.9 90.3 92.0 AD-11874 14.0 3.6 −0.6 63.74 36.6 41.1 21.2 AD-11875 37.1 22.5 9.9 92.11 54.4 52.0 47.5 76.56 AD-11876 11.8 4.2 1.3 5.85 35.7 43.8 50.3 AD-11878 3.5 −0.5 −1.7 65.6 62.4 60.0 AD-11879 30.5 21.5 3.8 93.89 −4.3 −19.3 11.4 80.10 AD-11882 16.0 12.4 5.1 80.92 9.1 4.8 19.5 77.03 AD-11883 13.2 6.8 1.4 −37.40 −29.3 12.5 26.9 −1048.33 AD-11884 23.7 11.4 5.5 25.83 41.4 25.2 40.9 −42.26 AD-11885 1.5 −0.8 −2.9 55.9 53.3 53.8 AD-11886 −1.2 −3.4 −4.7 38.7 47.2 67.9 AD-11887 16.6 4.6 −2.2 −85.11 69.8 54.1 54.1 85.65 AD-11888 12.9 3.8 2.3 62.2 66.5 65.7 AD-11889 12.2 5.9 −1.6 4.6 10.5 40.1 AD-11890 8.5 6.2 5.0 −41.7 −12.9 20.9 AD-11891 20.7 9.8 1.0 −69.47 19.3 23.9 32.0 AD-11892 −0.1 −2.5 −2.0 38.4 32.1 38.0 AD-11893 0.1 −2.1 −1.5 27.1 21.1 3.1 AD-11896 3.5 1.3 −1.6 23.3 −6.7 10.0 AD-11897 1.6 −1.3 −2.6 26.4 13.7 13.1 AD-11899 8.3 1.9 0.6 16.4 20.9 28.9 AD-11901 2.5 3.1 1.4 −89.3 71.9 78.6 AD-11902 5.9 0.6 −2.6 −15.2 62.9 79.8 AD-11903 1.1 −1.5 −3.6 64.0 45.9 45.9 AD-11904 0.7 0.4 −0.2 46.4 16.9 70.6 AD-11905 6.9 2.1 −0.1 −42.4 42.5 27.9 AD-11906 −0.4 0.3 −2.5 98.5 93.5 54.3 AD-11907 4.5 0.5 −1.1 95.8 45.3 95.1 AD-11908 −0.9 −1.7 0.2 39.0 86.6 84.5 AD-11909 7.0 2.9 1.1 79.1 −27.1 83.9 AD-11911 5.4 2.6 −1.9 97.4 98.6 94.0 AD-11912 −3.4 −4.5 −3.7 99.4 96.2 65.9 AD-11914 −0.6 −0.2 1.0 91.7 69.5 91.5 AD-11918 −6.3 −8.2 −6.7 −12.4 9.7 8.0 AD-11919 −1.0 −0.1 3.2 18.2 −9.2 32.5 AD-11925 3.5 1.9 −2.7 11.9 13.7 13.7 AD-11926 11.3 4.9 −3.2 46.95 16.9 37.0 66.5 93.16 AD-11927 −6.8 −8.4 −5.7 45.5 −12.2 −17.2 AD-11933 −0.2 1.4 3.3 −6.7 32.7 3.5 AD-11938 0.0 −2.4 −4.1 19.2 −45.8 1.4 AD-11939 −2.3 −2.0 −3.1 3.0 23.1 24.9 AD-11941 −8.3 −9.6 −7.5 42.1 4.0 −25.0 AD-11942 −4.4 −3.5 −2.5 31.6 2.5 1.4 AD-11943 1.9 0.7 −2.7 −5.6 20.5 15.4 AD-11944 −1.1 −2.1 −2.0 51.0 46.7 50.6 AD-11945 −7.7 −8.6 −5.9 77.2 30.5 55.8 AD-11946 0.6 0.8 −2.4 66.9 65.2 65.4 AD-11947 −0.6 −2.2 −4.1 66.6 68.5 68.5 AD-11948 −2.3 −4.0 −4.5 77.1 77.6 88.6 AD-11949 −6.6 −7.9 −6.4 67.5 33.7 2.9 AD-11950 −3.9 0.8 7.9 56.0 51.7 44.8 AD-11951 7.7 0.4 6.0 35.6 45.6 46.1 AD-11952 1.7 −4.5 −4.7 54.8 65.7 66.0 AD-11953 −9.1 −7.7 −6.8 51.4 22.8 30.1 AD-11954 −2.7 8.2 8.2 42.1 26.4 32.1 AD-11955 9.0 7.5 5.9 54.6 43.4 44.2 AD-11956 6.3 −6.5 −4.0 28.1 40.0 55.3 AD-11957 −1.9 −6.4 −2.8 78.2 95.9 69.2 AD-11958 2.0 1.2 −1.0 99.7 89.5 86.2 AD-11959 8.7 3.4 −1.2 81.2 74.5 74.5 AD-11960 2.8 1.7 0.2 71.9 61.4 82.7 AD-11961 −3.4 −5.5 −4.5 84.3 50.6 68.7 AD-11962 −1.4 0.0 −0.2 74.1 89.2 63.9 AD-11963 2.1 −0.3 −0.2 78.8 20.1 50.9 AD-11964 4.5 3.9 −0.1 61.5 51.0 58.4 AD-11965 −3.8 −6.3 −4.4 64.6 14.2 89.4 AD-11966 −0.5 −1.0 −0.5 49.5 −30.0 21.4 AD-11967 5.0 3.8 1.2 24.7 28.2 24.2 AD-11968 −0.8 −0.2 −0.3 9.5 6.5 26.5 AD-11969 3.9 0.6 −2.2 63.5 31.6 56.5 AD-11970 9.2 5.5 −1.6 47.6 36.9 57.1 AD-11971 −1.2 0.1 −1.7 63.8 55.3 55.3 AD-11972 2.7 −0.9 −0.8 66.7 82.1 78.1 AD-11973 3.2 5.3 −0.3 −137.3 −57.5 −69.7 AD-11974 1.7 2.3 2.6 −15.1 −41.3 −55.7 AD-11975 1.8 1.4 1.9 −63.6 −63.1 −54.6 AD-11976 2.3 2.7 2.7 −8.3 10.1 29.0 AD-11977 4.5 3.7 2.7 −168.8 −142.8 −116.4 AD-11978 2.1 1.2 0.8 −66.5 −91.0 −120.2 AD-11979 −1.7 −2.0 −2.2 −140.3 −128.4 −107.4 AD-11980 −1.3 −0.8 −0.6 −21.5 −10.2 −14.2 AD-11981 9.1 6.7 4.6 −181.1 −162.1 −164.3 AD-11982 −0.2 −0.4 −1.4 −189.5 −148.6 −159.6 AD-11983 −2.7 −3.4 −3.7 −131.3 −111.7 −115.3 AD-11984 −1.9 −0.5 0.1 −36.1 −12.9 −10.8 AD-11985 5.5 6.4 2.8 −139.4 −160.3 −216.6 AD-11986 6.1 6.0 5.8 −111.7 −143.8 −134.7 AD-11987 0.9 1.5 2.0 −162.1 −148.5 −132.2 AD-11988 7.4 8.5 8.9 −196.2 −201.7 −178.2 AD-11989 1.9 2.0 1.6 −62.4 −57.6 −61.2 AD-11990 0.8 −0.2 −0.8 −51.3 −69.3 −76.8 AD-11991 −1.9 −2.4 −2.3 −84.5 −65.2 −51.0 AD-11992 0.6 1.3 1.6 −83.1 −60.4 −57.1 AD-11993 6.6 5.6 3.7 −29.9 −33.8 −35.4 AD-11994 0.3 0.1 −0.6 −60.1 −59.5 −59.4 AD-11995 −2.3 −2.1 −1.9 −73.2 −61.7 −58.5 AD-11996 −0.7 0.3 0.4 −4.6 −14.0 −21.4 AD-11997 4.1 4.3 −0.1 64.7 26.4 52.9 AD-11998 0.3 0.0 −0.7 69.1 61.0 52.1 AD-11999 −0.5 −0.1 0.1 31.9 37.3 39.5 AD-12000 −0.8 0.2 0.8 51.7 54.7 60.6 AD-12001 3.7 3.3 2.9 54.7 49.4 47.3 AD-12002 3.8 2.9 2.2 34.0 49.3 62.0 AD-12003 −0.3 −0.4 −0.2 26.3 29.4 32.9 AD-12004 0.6 0.8 1.4 37.7 36.6 36.9 AD-12005 4.9 4.7 3.9 19.6 9.3 7.5 AD-12006 0.8 0.5 0.5 −22.4 −23.6 −19.4 AD-12007 −1.3 −0.7 −0.3 −10.4 −13.6 −21.7 AD-12008 0.7 1.4 1.4 31.6 31.4 33.4 AD-12009 0.8 2.5 −2.2 36.9 25.4 31.0 AD-12010 −1.2 −1.5 −1.6 35.6 23.9 15.8 AD-12011 −1.2 −0.3 0.2 50.4 46.0 41.7 AD-12012 0.7 0.7 0.5 47.1 49.2 51.5 AD-12013 1.3 1.1 −0.5 31.5 25.2 21.8 AD-12014 −1.8 −3.0 −2.7 21.5 26.1 26.3 AD-12015 −4.2 −4.1 −3.8 36.5 35.7 34.2 AD-12016 −1.9 −1.5 −1.2 38.7 41.0 41.9 AD-12017 −0.4 −1.0 −2.2 6.4 12.0 17.5 AD-12018 −1.0 −2.6 −2.9 −19.0 −8.5 −7.1 AD-12019 −3.1 −2.7 −2.3 −3.4 −3.2 0.0 AD-12020 −2.1 −1.4 −1.0 2.2 10.2 12.7 AD-12021 4.9 3.3 2.1 −34.2 −9.2 −30.6 AD-12022 3.9 3.1 2.1 −139.2 −184.9 −191.4 AD-12023 0.4 0.5 0.8 10.7 11.7 −2.8 AD-12024 0.2 1.4 2.3 −8.4 6.0 18.1 AD-12025 6.9 4.8 3.2 18.0 −1.4 −25.4 AD-12026 −0.3 −0.1 0.2 −79.8 −64.2 −44.8 AD-12027 −0.8 −1.0 −0.5 −28.2 −43.7 −57.1 AD-12028 −1.2 −0.2 0.8 −8.1 −0.6 6.2 AD-12029 6.9 5.6 3.8 −65.2 −79.3 −106.3 AD-12030 −0.1 −0.8 −2.0 −70.4 −93.2 −119.7 AD-12031 0.2 0.1 −0.1 −32.4 −34.4 −34.9 AD-12032 0.0 0.1 0.6 −86.6 −68.5 −43.4 AD-12033 −4.7 −8.2 −7.6 −115.7 −149.7 −58.5 AD-12034 −6.0 −5.7 −5.7 −217.6 −210.8 −215.6 AD-12035 −7.7 −7.4 −7.6 −99.6 −102.4 −107.1 AD-12036 −6.6 −6.1 −5.1 −111.1 −91.0 −89.8 AD-12037 −7.8 −7.8 −7.7 45.1 −5.3 −44.2 AD-12462 −8.4 −8.6 −9.4 −150.2 −135.8 −130.8 AD-12463 −8.3 −8.4 −8.6 −70.1 −70.9 −75.8 AD-12464 −6.3 −6.6 −6.5 −38.9 −19.7 −2.6 AD-12465 −2.8 −3.8 −5.3 −52.8 −75.2 −92.9 AD-12466 −1.9 −3.1 −3.5 −68.5 −103.9 −113.9 AD-12467 −5.9 −5.8 −5.6 −118.6 −121.8 −117.7 AD-12468 −4.9 −4.2 −3.3 −14.2 −8.4 −6.8 AD-12469 −4.8 −6.0 −6.6 −29.1 −6.1 −10.2 AD-12470 −0.9 −1.4 −1.9 −39.5 −19.2 −1.8 AD-12471 −4.0 −4.0 −4.0 −15.4 −16.3 −17.3 AD-12472 −3.2 −3.4 −2.6 25.9 24.0 27.4 AD-12473 −3.5 −3.8 −4.1 −42.5 −31.5 −26.4 AD-12474 −5.0 −5.3 −5.8 −7.1 −3.0 −1.8 AD-12475 −7.1 −7.6 −7.4 −10.2 −4.3 −0.7 AD-12476 −5.2 −4.7 −3.5 24.3 26.9 32.2 AD-12477 −2.8 −3.8 −4.4 −41.4 −45.4 −37.6 AD-12478 −7.3 −7.6 −7.8 −59.7 −63.8 −67.5 AD-12479 −7.9 −8.3 −8.1 −54.9 −39.3 −8.6 AD-12480 −2.7 −2.4 −1.4 9.3 18.0 12.4 AD-12481 −5.7 −5.5 −7.5 −131.4 −152.8 −48.2 AD-12482 −4.4 −4.5 −4.1 −159.1 −127.8 −140.7 AD-12483 −4.8 −4.8 −4.5 −66.0 −64.8 −60.3 AD-12484 −4.2 −3.9 −3.8 17.9 27.6 29.1 AD-12485 −2.7 −4.0 −5.4 −170.2 −176.6 −186.0 AD-12486 −8.5 −8.6 −8.6 −200.1 −194.6 −169.0 AD-12487 −8.1 −8.0 −7.8 −117.5 −106.8 −86.5 AD-12488 −8.2 −7.9 −7.8 −17.3 −13.1 0.8 AD-12489 −4.2 −5.6 −7.1 −128.0 −152.3 −185.8 AD-12490 −8.6 −8.9 −8.8 −241.7 −258.1 −251.4 AD-12491 −8.9 −9.0 −8.4 −181.6 −184.9 −188.0 AD-12492 −8.6 −7.7 −6.7 −23.3 −22.4 −27.3 AD-12493 −8.2 −6.7 −4.5 −93.8 −54.8 6.7 AD-12494 −7.6 −8.0 −8.2 −62.2 −63.5 −54.7 AD-12495 −6.6 −5.5 −4.9 16.6 0.4 −10.0 AD-12496 −4.1 −4.2 −3.8 40.2 41.7 39.5 AD-12497 −5.1 −5.2 −6.3 −67.9 −65.2 −67.3 AD-12498 −5.8 −6.0 −6.4 −68.6 −84.1 −94.1 AD-12499 −6.6 −6.3 −6.3 −93.4 −80.2 −61.0 AD-12500 −6.0 −5.4 −4.7 9.7 10.2 11.3 AD-12501 −4.8 −5.0 −5.8 −87.1 −108.5 −110.6 AD-12502 −6.8 −7.2 −6.7 −126.5 −125.5 −119.1 AD-12503 −10.4 −9.6 −9.9 −85.2 −76.4 −86.7 AD-12504 −4.0 −3.6 −2.5 −59.7 −52.7 −34.7 AD-12505 18.1 −0.9 −5.5 42.18 3.5 −116.5 −34.2 −282.78 AD-12506 −2.1 −2.7 −4.2 −29.8 −22.3 −11.9 AD-12507 −1.7 7.2 15.0 44.47 29.1 33.0 32.3 AD-12508 −4.2 −3.2 −1.9 40.7 33.9 30.5 AD-12509 −9.2 −8.9 −8.2 −54.3 −67.7 −80.3 AD-12510 −7.9 −7.6 −7.6 −127.6 −117.5 −124.2 AD-12511 −7.1 −6.9 −6.8 −28.4 −18.6 −6.7 AD-12512 −5.2 −4.1 −3.3 −0.4 −1.7 −1.5 AD-12513 −6.9 −7.4 −8.8 −65.5 −80.0 −100.6 AD-12514 −10.8 −11.0 −10.6 −83.8 −85.0 −92.0 AD-12515 −10.7 −9.6 −9.3 −19.3 −41.2 −32.7 AD-12516 −5.8 −5.3 −4.2 −5.9 0.9 15.9 AD-12517 −8.6 −8.7 −7.1 29.2 53.0 49.4 AD-12518 −8.3 −8.0 −8.0 65.7 57.8 53.6 AD-12519 −7.2 −7.2 −7.6 51.2 51.3 53.9 AD-12520 −7.0 −6.3 −5.4 67.7 73.2 78.8 AD-12521 −6.4 −8.0 −9.1 19.8 27.6 35.5 AD-12522 −9.9 −9.0 −9.1 50.3 43.0 34.3 AD-12523 −9.0 −8.7 −8.9 28.3 31.9 38.1 AD-12524 −7.0 −7.4 −7.0 63.7 67.1 65.9 AD-12525 −1.6 −3.8 −6.0 16.1 21.8 21.2

TABLE 4 In vitro Plaque assay controls (all values average of 3-4 experiments and expressed as % inhibition relative to no siRNA treatment) AD-1955 (luc) 31.37 10.97 AD-5179 (GFP) 15.15 18.65 LS L#1 77.23 N/A LS NP#1 73.94 N/A LS VP35#1 67.27 N/A

TABLE 5 Exo + endo seq seq parent light id   id duplex duplex Target sense antisense no sense 5′-3′ no antisense 5′-3′ AD-11594 AD-3542 NP A- A-30769  995 cAGuAGGAcAcAuGAuGGudTsdT  996 ACcAUcAUGUGUCCuACUGdTsdT 30768 AD-11596 AD-3543 NP A- A-30771  997 GuAGGAcAcAuGAuGGuGAdTsdT  998 UcACcAUcAUGUGUCCuACdTsdT 30770 AD-11597 AD-3544 NP A- A-30773  999 uAGGAcAcAuGAuGGuGAudTsdT 1000 AUcACcAUcAUGUGUCCuAdTsdT 30772 AD-11598 AD-3545 NP A- A-30775 1001 GAuGGuGAuuuuccGuuuGdTsdT 1002 cAAACGGAAAAUcACcAUCdTsdT 30774 AD-11600 AD-3546 NP A- A-30777 1003 uGGuGAuuuuccGuuuGAudTsdT 1004 AUcAAACGGAAAAUcACcAdTsdT 30776 AD-11603 AD-3547 NP A- A-30779 1005 cuGAGAAGcAAcuccAAcAdTsdT 1006 UGUUGGAGUUGCUUCUcAGdTsdT 30778 AD-11604 AD-3548 NP A- A-30781 1007 uGAGAAGcAAcuccAAcAAdTsdT 1008 UUGUUGGAGUUGCUUCUcAdTsdT 30780 AD-11606 AD-3549 NP A- A-30783 1009 AGAAGcAAcuccAAcAAuAdTsdT 1010 uAUUGUUGGAGUUGCUUCUdTsdT 30782 AD-11609 AD-3550 VP35 A- A-30785 1011 AAGuGAuGAAGAuuAAGAAdTsdT 1012 UUCUuAAUCUUcAUcACUUdTsdT 30784 AD-11610 AD-3551 VP35 A- A-30787 1013 AGuGAuGAAGAuuAAGAAAdTsdT 1014 UUUCUuAAUCUUcAUcACUdTsdT 30786 AD-11611 AD-3552 VP40 A- A-30789 1015 cuGccuGcuGcAAcAuGGAdTsdT 1016 UCcAUGUUGcAGcAGGcAGdTsdT 30788 AD-11613 AD-3553 GP A- A-30791 1017 GGcuGAAAAcuGcuAcAAudTsdT 1018 AUUGuAGcAGUUUUcAGCCdTsdT 30790 AD-11614 AD-3554 GP A- A-30793 1019 GcuGAAAAcuGcuAcAAucdTsdT 1020 GAUUGuAGcAGUUUUcAGCdTsdT 30792 AD-11615 AD-3555 GP A- A-30795 1021 cuGAAAAcuGcuAcAAucudTsdT 1022 AGAUUGuAGcAGUUUUcAGdTsdT 30794 AD-11618 AD-3556 GP A- A-30797 1023 AAAAcuGcuAcAAucuuGAdTsdT 1024 UcAAGAUUGuAGcAGUUUUdTsdT 30796 AD-11621 AD-3557 GP A- A-30799 1025 AcuGcuAcAAucuuGAAAudTsdT 1026 AUUUcAAGAUUGuAGcAGUdTsdT 30798 AD-11622 AD-3558 VP30 A- A-30801 1027 AGcAAAuccAAcGGcuGAudTsdT 1028 AUcAGCCGUUGGAUUUGCUdTsdT 30800 AD-11624 AD-3559 VP30 A- A-30803 1029 cAAAuccAAcGGcuGAuGAdTsdT 1030 UcAUcAGCCGUUGGAUUUGdTsdT 30802 AD-11627 AD-3560 L A- A-30805 1031 AuGcAuGucAGuGAuuAuudTsdT 1032 AAuAAUcACUGAcAUGcAUdTsdT 30804 AD-11628 AD-3561 L A- A-30807 1033 uGcAuGucAGuGAuuAuuAdTsdT 1034 uAAuAAUcACUGAcAUGcAdTsdT 30806 AD-11629 AD-3562 L A- A-30809 1035 GcAuGucAGuGAuuAuuAudTsdT 1036 AuAAuAAUcACUGAcAUGCdTsdT 30808 AD-11630 AD-3563 L A- A-30811 1037 cAuGucAGuGAuuAuuAuAdTsdT 1038 uAuAAuAAUcACUGAcAUGdTsdT 30810 AD-11631 AD-3564 L A- A-30813 1039 AuGucAGuGAuuAuuAuAAdTsdT 1040 UuAuAAuAAUcACUGAcAUdTsdT 30812

TABLE 6 In vitro plaque In vitro plaque assay against assay against In vitro Ebola-Zaire Ebola-Sudan plasmid (% inhibition (% inhibition modified screen IC50 relative to no relative to no duplex (nM) siRNA) siRNA) AD-3542 1.60 84% 74% AD-3543 0.00 74% 77% AD-3544 0.61 65% 13% AD-3545 0.00 82% 61% AD-3546 1.35 88% 71% AD-3547 0.00 81% 26% AD-3548 7.82 68% 73% AD-3549 0.00 68% 74% AD-3550 0.17 77% 22% AD-3551 0.08 2% 75% AD-3552 0.00 78% 70% AD-3553 0.19 85% 26% AD-3554 0.77 84% 15% AD-3555 0.88 −5% 19% AD-3556 0.00 73% 74% AD-3557 0.21 100% 28% AD-3558 0.00 −7% 68% AD-3559 0.00 −252% −7% AD-3560 0.50 16% −35% AD-3561 0.00 −105% 19% AD-3562 0.00 −75% 63% AD-3563 5.42 73% −17% AD-3564 0.97 −86% 19% AD-3621 0.00 80% 48% AD-3622 16.00 61% 47% AD-3623 0.00 98% 37% AD-3624 0.00 84% 24% AD-3625 0.00 −7% −5% AD-3626 0.00 53% 31%

TABLE 7 IFN induction TNF induction normalized normalized to positive to positive control siRNA control siRNA duplex % of control duplex % of control AD-11546 131.6 AD-11546 30.1 AD-11558 98.8 AD-11558 57.2 AD-11570 0 AD-11570 0 AD-11588 147 AD-11588 0.0 AD-11590 0.0 AD-11590 130.5 AD-11594 17.8 AD-11594 124.8 AD-11597 22.0 AD-11597 242.9 AD-11598 25.7 AD-11598 180.3 AD-11599 136 AD-11599 183.9 AD-11600 13.5 AD-11600 141.0 AD-11603 69.0 AD-11603 81.4 AD-11606 33.2 AD-11606 79.8 AD-11609 126.9 AD-11609 46.3 AD-11610 138.2 AD-11610 48.5 AD-11611 43.2 AD-11611 41.0 AD-11613 167.0 AD-11613 52.6 AD-11614 162.1 AD-11614 48.1 AD-11615 171.2 AD-11615 60.0 AD-11618 137.3 AD-11618 54.6 AD-11621 0.0 AD-11621 325.8 AD-11622 37.2 AD-11622 28.5 AD-11623 58.0 AD-11623 26.0 AD-11624 63.2 AD-11624 29.2 AD-11627 6.4 AD-11627 125.0 AD-11628 0.0 AD-11628 101.1 AD-11630 0.0 AD-11630 170.3 AD-11631 0.0 AD-11631 156.0 AD-11644 0 AD-11644 0.0 AD-11650 0.0 AD-11650 0.0 AD-11659 0.0 AD-11659 69.0 AD-11673 9.2 AD-11673 0.0 AD-11678 0.0 AD-11678 0.0 AD-11683 0.0 AD-11683 19.6 AD-11684 0.0 AD-11684 24.3 AD-11691 0 AD-11691 0.0 AD-11695 0.0 AD-11695 5.2 AD-11698 5.3 AD-11698 14.0 AD-11706 0.0 AD-11706 0.0 AD-11707 0 AD-11707 0.0 AD-11710 0 AD-11710 0.0 AD-11721 0.0 AD-11721 0.0 AD-11725 0.0 AD-11725 0.0 AD-11732 0.0 AD-11732 0.0 AD-11743 16.1 AD-11743 0.0 AD-11756 0.0 AD-11756 0.0 AD-11757 0.0 AD-11757 0.0 AD-11758 0.0 AD-11758 0.0 AD-11759 0.0 AD-11759 0.0 AD-11773 0.0 AD-11773 0.0 AD-11780 0.0 AD-11780 7.9 AD-11789 0.0 AD-11789 5.7 AD-11804 0.0 AD-11804 0.0 AD-11811 0.0 AD-11811 0.0 AD-11814 0.0 AD-11814 0.0 AD-11816 0.0 AD-11816 0.0 AD-11822 9.8 AD-11822 0.0 AD-11823 0.0 AD-11823 0.0 AD-11832 0.0 AD-11832 0.0 AD-11836 0.0 AD-11836 0.0 AD-11939 0.0 AD-11939 0.0 AD-11976 0.0 AD-11976 0.0 AD-11982 6.9 AD-11982 15.1 AD-11990 12.2 AD-11990 0.0 AD-11992 7.3 AD-11992 0.0 AD-12007 0.0 AD-12007 0.0 AD-12013 0.0 AD-12013 0.0 AD-12019 24.6 AD-12019 5.0 AD-12024 0.0 AD-12024 19.8 AD-12035 0.0 AD-12035 8.5 AD-12475 0.0 AD-12475 0.0 AD-12484 21.0 AD-12484 9.5 AD-12491 0.0 AD-12491 13.1 AD-12500 12.6 AD-12500 53.3 AD-12502 101.6 AD-12502 55.5 AD-3542 0.0 AD-3542 0.0 AD-3543 0.0 AD-3543 0.0 AD-3544 10.1 AD-3544 0.0 AD-3545 11.8 AD-3545 0.0 AD-3546 0.0 AD-3546 0.0 AD-3547 0.0 AD-3547 31.0 AD-3548 0.0 AD-3548 5.9 AD-3549 0.0 AD-3549 10.8 AD-3550 7.4 AD-3550 0.0 AD-3551 0.0 AD-3551 0.0 AD-3552 0.0 AD-3552 0.0 AD-3553 0.0 AD-3553 0.0 AD-3554 0.0 AD-3554 11.5 AD-3555 0.0 AD-3555 6.2 AD-3556 0.0 AD-3556 9.1 AD-3557 0.0 AD-3557 0.0 AD-3558 0.0 AD-3558 5.8 AD-3559 0.0 AD-3559 5.3 AD-3560 0.0 AD-3560 0.0 AD-3561 0.0 AD-3561 0.0 AD-3562 0.0 AD-3562 0.0 AD-3563 0.0 AD-3563 0.0 AD-3564 0.0 AD-3564 0.0 AD-3621 0.0 AD-3621 0.0 AD-3622 0.0 AD-3622 0.0 AD-3623 5.7 AD-3623 0.0 AD-3624 10.0 AD-3624 0.0 AD-3625 0.0 AD-3625 0.0 AD-3626 0.0 AD-3626 0.0

TABLE 8 In vitro plasmid In vitro screen plasmid single dose screen duplex (% IC50 name silencing) (nM) AD-11542 9% AD-11543 −3% AD-11544 −1% AD-11545 13% AD-11546 68% 0.72 AD-11547 28% AD-11548 48% AD-11549 43% AD-11550 −5% AD-11551 8% AD-11552 −17% AD-11553 −6% AD-11554 15% AD-11555 2% AD-11556 6% AD-11557 −6% AD-11558 70% 0.46 AD-11559 28% AD-11560 5% AD-11561 30% AD-11562 24% AD-11563 6% AD-11564 0% AD-11565 −4% AD-11566 4% AD-11567 −2% AD-11568 0% AD-11569 12% AD-11570 73% 0.95 AD-11571 −2% AD-11572 −3% AD-11573 2% AD-11574 15% AD-11575 −2% AD-11576 −9% AD-11577 −9% AD-11578 77% AD-11579 37% AD-11580 35% AD-11581 60% AD-11582 21% AD-11583 47% AD-11584 0% AD-11585 −1% AD-11586 36% AD-11587 66% AD-11588 47% AD-11589 77% AD-11590 83% 0.57 AD-11591 65% AD-11592 62% AD-11593 55% AD-11594 85% 0.35 AD-11595 72% AD-11596 84% 0.24 AD-11597 85% 0.33 AD-11598 87% 0.21 AD-11599 91% 0.81 AD-11600 89% 0.29 AD-11601 84% 1.07 AD-11602 71% AD-11603 80% 1.3 AD-11604 81% 1.44 AD-11605 75% AD-11606 78% 6.38 AD-11607 53% AD-11608 60% AD-11609 75% 0.3 AD-11610 74% 0.15 AD-11611 61% 0.28 AD-11612 −5% AD-11613 84% 0.077 AD-11614 85% 0.102 AD-11615 79% 0.211 AD-11616 66% AD-11617 59% AD-11618 78% 0.24 AD-11619 57% AD-11620 64% AD-11621 74% 0.15 AD-11622 70% 0.41 AD-11623 67% 0.54 AD-11624 75% 0.15 AD-11625 11% AD-11626 51% AD-11627 71% 0.28 AD-11628 68% 0.33 AD-11629 75% 0.18 AD-11630 73% 0.24 AD-11631 69% 0.31 AD-11632 53% AD-11633 63% 1.78 AD-11634 65% 0.76 AD-11635 29% AD-11636 43% AD-11637 −5% AD-11638 6% AD-11639 2% AD-11640 38% AD-11641 35% AD-11642 55% AD-11643 33% AD-11644 36% AD-11645 45% AD-11646 37% AD-11647 41% AD-11648 61% AD-11649 35% AD-11650 84% 0.7 AD-11651 13% AD-11652 64% AD-11653 61% AD-11654 6% AD-11655 59% AD-11656 38% AD-11657 39% AD-11658 59% AD-11659 82% 0.038 AD-11660 39% AD-11661 −5% AD-11662 −1% AD-11663 14% AD-11664 19% AD-11665 7% AD-11666 −4% AD-11667 −14% AD-11668 63% AD-11669 28% AD-11670 23% AD-11671 23% AD-11672 15% AD-11673 79% 0.117 AD-11674 67% AD-11675 46% AD-11676 20% AD-11677 34% AD-11678 79% 0.149 AD-11679 51% AD-11680 24% AD-11681 72% AD-11682 73% AD-11683 88% 0.056 AD-11684 80% 0.184 AD-11685 33% AD-11686 72% AD-11687 32% AD-11688 15% AD-11689 58% AD-11690 26% AD-11691 60% AD-11694 54% AD-11695 81% 0.46 AD-11696 32% AD-11698 73% 0.2 AD-11700 −9% AD-11704 35% AD-11705 39% AD-11706 67% 0.56 AD-11707 2% AD-11708 −10% AD-11710 65% 4.57 AD-11711 −3% AD-11712 17% AD-11713 0% AD-11714 42% AD-11715 41% AD-11716 18% AD-11717 32% AD-11718 −3% AD-11719 36% AD-11720 41% AD-11721 68% 1.35 AD-11722 31% AD-11723 49% AD-11724 27% AD-11725 67% 0.34 AD-11726 12% AD-11727 3% AD-11728 5% AD-11729 12% AD-11730 6% AD-11731 63% 49.4 AD-11732 76% 2.88 AD-11733 60% 8.76 AD-11734 44% AD-11735 17% AD-11736 44% AD-11737 14% AD-11738 −9% AD-11739 23% AD-11740 1% AD-11741 9% AD-11742 40% AD-11743 77% 0.11 AD-11744 24% AD-11745 27% AD-11746 −9% AD-11747 16% AD-11748 8% AD-11749 AD-11750 33% AD-11751 19% AD-11752 61% 6.92 AD-11753 13% AD-11754 53% AD-11755 AD-11756 61% 1.21 AD-11757 63% 1.57 AD-11758 28% AD-11759 66% 1.61 AD-11760 64% 3.4 AD-11761 59% AD-11762 54% AD-11763 47% AD-11764 21% AD-11765 −1% AD-11766 −1% AD-11767 67% 4.4 AD-11768 52% AD-11769 21% AD-11770 55% AD-11771 36% AD-11772 41% AD-11773 76% 0.37 AD-11774 35% AD-11775 49% AD-11776 50% AD-11777 −5% AD-11778 18% AD-11779 15% AD-11780 62% 0.76 AD-11781 14% AD-11782 38% AD-11783 46% AD-11784 23% AD-11785 −11% AD-11786 42% AD-11787 48% AD-11788 19% AD-11789 64% 0.38 AD-11790 26% AD-11791 22% AD-11792 −8% AD-11793 26% AD-11794 57% AD-11795 AD-11796 59% AD-11797 11% AD-11798 11% AD-11799 35% AD-11800 2% AD-11801 −6% AD-11802 0% AD-11803 5% AD-11804 88% 0.281 AD-11805 5% AD-11806 9% AD-11807 6% AD-11808 50% AD-11809 24% AD-11810 −1% AD-11811 66% 1.56 AD-11812 1% AD-11813 17% AD-11814 65% 0.43 AD-11815 −1% AD-11816 65% 0.99 AD-11817 67% 2.98 AD-11818 44% AD-11819 64% AD-11820 36% AD-11821 64% AD-11822 62% 1.44 AD-11823 69% 0.32 AD-11824 38% AD-11825 18% AD-11826 23% AD-11827 2% AD-11828 51% AD-11829 AD-11830 46% AD-11831 20% AD-11832 71% 0.94 AD-11833 3% AD-11834 23% AD-11835 −8% AD-11836 65% 1.46 AD-11837 26% AD-11838 −16% AD-11839 22% AD-11840 −5% AD-11841 60% AD-11842 19% AD-11843 57% AD-11844 18% AD-11845 8% AD-11846 48% AD-11847 57% AD-11848 2% AD-11849 66% 0.32 AD-11850 25% AD-11851 −12% AD-11852 27% AD-11853 28% AD-11854 55% AD-11855 43% AD-11856 −20% AD-11857 61% 3.28 AD-11858 6% AD-11859 4% AD-11860 79% AD-11861 31% AD-11862 48% AD-11863 85% 0.39 AD-11864 42% AD-11865 37% AD-11870 34% AD-11871 79% 0.63 AD-11872 70% AD-11873 70% AD-11874 39% AD-11875 39% AD-11876 34% AD-11878 −1% AD-11879 50% AD-11882 −6% AD-11883 11% AD-11884 7% AD-11885 −3% AD-11886 −5% AD-11887 18% AD-11888 41% AD-11889 1% AD-11890 44% AD-11891 20% AD-11892 37% AD-11893 29% AD-11896 1% AD-11897 41% AD-11899 12% AD-11901 −2% AD-11902 40% AD-11903 14% AD-11904 1% AD-11905 33% AD-11906 2% AD-11907 9% AD-11908 5% AD-11909 16% AD-11911 37% AD-11912 19% AD-11914 19% AD-11918 1% AD-11919 −1% AD-11925 −5% AD-11926 60% AD-11927 −11% AD-11933 30% AD-11938 6% AD-11939 71% 0.48 AD-11941 47% AD-11942 33% AD-11943 48% AD-11944 51% AD-11945 69% AD-11946 39% AD-11947 39% AD-11948 83% 0.68 AD-11949 41% AD-11950 73% AD-11951 55% AD-11952 81% 1.42 AD-11953 52% AD-11954 55% AD-11955 79% 0.63 AD-11956 37% AD-11957 39% AD-11958 34% AD-11959 36% AD-11960 19% AD-11961 −4% AD-11962 −6% AD-11963 3% AD-11964 13% AD-11965 28% AD-11966 −4% AD-11967 15% AD-11968 4% AD-11969 0% AD-11970 −7% AD-11971 3% AD-11972 58% AD-11973 4% AD-11974 38% AD-11975 −11% AD-11976 63% 0.21 AD-11977 2% AD-11978 56% AD-11979 5% AD-11980 5% AD-11981 19% AD-11982 65% 0.14 AD-11983 52% AD-11984 50% AD-11985 50% AD-11986 6% AD-11987 −7% AD-11988 58% AD-11989 27% AD-11990 72% 0.24 AD-11991 29% AD-11992 76% 0.94 AD-11993 46% AD-11994 21% AD-11995 −3% AD-11996 53% AD-11997 0% AD-11998 3% AD-11999 19% AD-12000 41% AD-12001 3% AD-12002 37% AD-12003 17% AD-12004 5% AD-12005 6% AD-12006 69% AD-12007 81% 0.268 AD-12008 35% AD-12009 22% AD-12010 34% AD-12011 10% AD-12012 25% AD-12013 75% 0.60 AD-12014 29% AD-12015 4% AD-12016 2% AD-12017 5% AD-12018 7% AD-12019 79% 0.904 AD-12020 6% AD-12021 0% AD-12022 2% AD-12023 16% AD-12024 87% 0.075 AD-12025 4% AD-12026 5% AD-12027 66% AD-12028 24% AD-12029 −8% AD-12030 46% AD-12031 48% AD-12032 −10% AD-12033 64% 6.74 AD-12034 45% AD-12035 70% 0.11 AD-12036 43% AD-12037 AD-12462 35% AD-12463 39% AD-12464 47% AD-12465 34% AD-12466 35% AD-12467 25% AD-12468 −9% AD-12469 −3% AD-12470 50% AD-12471 12% AD-12472 9% AD-12473 52% AD-12474 1% AD-12475 62% 0.13 AD-12476 19% AD-12477 −12% AD-12478 5% AD-12479 21% AD-12480 13% AD-12481 22% AD-12482 65% AD-12483 78% AD-12484 90% 0.023 AD-12485 76% AD-12486 13% AD-12487 60% AD-12488 54% AD-12489 11% AD-12490 72% AD-12491 86% 0.047 AD-12492 41% AD-12493 26% AD-12494 12% AD-12495 69% AD-12496 44% AD-12497 2% AD-12498 14% AD-12499 63% AD-12500 86% 0.057 AD-12501 57% AD-12502 88% 0.048 AD-12503 −2% AD-12504 8% AD-12505 29% AD-12506 31% AD-12507 48% AD-12508 47% AD-12509 2% AD-12510 −21% AD-12511 28% AD-12512 43% AD-12513 −22% AD-12514 38% AD-12515 −9% AD-12516 58% AD-12517 18% AD-12518 −8% AD-12519 −5% AD-12520 62% 1.12 AD-12521 −12% AD-12522 53% AD-12523 55% AD-12524 60% AD-12525 32%

TABLE 9 WBC Platelets Lymphocyte # Animal #1 day 0 7.1 328 2 (AD-11570 day 3 6.9 308 1.9 treatment) day 5 6.2 394 3.4 Animal #2 day 0 3.6 299 1.5 (AD-11570 day 3 10.9 254 1.5 treatment) day 5 12.9 281 1.8 day 8 21.2 444 4.3 Animal #3 day 0 3.2 218 2.2 (AD-11570 day 3 10.9 202 1.9 treatment) day 5 6.4 266 2.4 day 8 18.5 306 3.6 Animal #4 day 0 9.7 398 7.3 (untreated) day 3 8.4 448 4.4 day 5 6.2 263 1.9 day 8 2.8 143 1.5

TABLE 10 Summary of Guinea Pig Study Dosing Regimen Dose Treatment Dose/group Group siRNA Formulation (mg/kg) Route on days Number (mg) 1 AD-11570 LNP09 2-3 IP 0, 3, 6 8 36 2 AD-11570 DODMA 2-3 IP 0, 3, 6 8 36 3 AD-1955 LNP09 2-3 IP 0, 3, 6 8 36 4 AD-1955 DODMA 2-3 IP 0, 3, 6 8 36 5 saline — — IP 0, 3, 6 8 36

TABLE 11 Summary of Guinea Pig Study with Different Dosing Regimens Dose Treatment on Group siRNA Formulation (mg/kg) route days N 1 AD-11570 LNP09 3 IP 0, 2, 4, 6, 8 8 2* AD-11570 LNP09 1 IP Daily (0-8) 8 3# AD-11570 LNP09 1 IP Daily (0-8) 8 4 AD-1955 LNP09 3 IP 0, 2, 4, 6, 8 8 5 AD-1955 LNP09 1 IP Daily (0-8) 8 6 Saline — — IP Daily (0-8) 8 *Group 2 animals are dosed with siRNA at 2 hours prior to virus infection for the Day 0 dose. #Group 3 animals are dosed with siRNA 30 minutes after virus infection for the Day 0 dose.

TABLE 12 # of guinea Group siRNA formulation Route Dose and timing pigs 1 11570 P/Q IV 3 mg/kg, 0, 2, 4, dpc 5 2 11570 E/F IV 3 mg/kg, 0, 2, 4, dpc 8 3 1955 E/F IV 3 mg/kg, 0, 2, 4, dpc 3 4 11570 E/F IP 3 mg/kg, 0, 2, 4, dpc 8 5 PBS IP 0, 2, 4, dpc 8

TABLE 13 # of Group siRNA Formulation Route Dose Regimen GP 1 11570 E/F IV 3 mg/kg D 0, 2, 4 6 2 11570 E/F IV 1 mg/kg D 0, 2, 4 6 3 11570 E/F IV 0.3 mg/kg   D 0, 2, 4 6 4  1955 E/F IV 3 mg/kg D 0, 2, 4 5 5 N/A N/A D 0, 2, 4 8

TABLE 14 Group siRNA Formulation Route Dose Regimen # of GP 1 11570 Lipid D IV 0.3 mg/kg D 0, 2, 4 6 2 11570 Lipid T IV 0.3 mg/kg D 0, 2, 4 6 3 11570 Lipid M IV 0.3 mg/kg D 0, 2, 4 6 4 11570 Lipid D IV   1 mg/kg D 0, 2, 4 5 5 N/A N/A D 0, 2, 4 7

TABLE 15 2^(nd) # Formu- and 3^(rd) of Group siRNA lation Route Dose 1^(st) dose dose GP 1 11570 E/F IV 3 mg/kg Day 0, 1 hr 2, 4, 6 before dpc virus 2 11570 E/F IV 3 mg/kg Day 0, 1 hr 2, 4, 6 after virus dpc 3 11570 E/F IV 3 mg/kg Day 1, 24 hr 2, 4, 6 after dpc virus 4 11570 E/F IV 3 mg/kg Day 2 48 hr 4, 6, 6 after virus dpc 5 PBS IP 0 4

TABLE 16 # of Formu- Dose and guinea Group Treatment lation Route Regimen* pigs Challenge 1 11570 Lipid D IV 3 mg/kg, 12 100 pfu E/F 0, 2, 4, dpc EBOV 2  1955 Lipid D IV 3 mg/kg, 8 100 pfu E/F 0, 2, 4, dpc EBOV 3 PBS None IP 0, 2, 4, dpc 8 100 pfu EBOV 4 None None None None 8 100 pfu EBOV 5 Naïve None None None 4 None

TABLE 17 Group # Treatment day 5 day 7 day 10 1 11570 n = 4 n = 4 n = 4 2 1955 n = 4 n = 4 3 PBS n = 4 n = 4 5 Naïve n = 4

NP Chimeric sequence (SEQ ID NO: 1043): GGTACCCTCGAGGAGGAAGATTAATAATTTTCCTCTCATTGAAATTTATATCGGAATTTAAATTG AAATTGTTACTGTAATCACACCTGGTTTGTTTCAGAGCCACATCACAAAGATAGAGAACAACCTA GGTCTCCGAAGGGAGCAAGGGCATCAGTGTGCTCAGTTGAAAATCCCTTGTCAACACCTAGGTCT TATCACATCACAAGTTCCACCTCAGACTCTGCAGGGTGATCCAACAACCTTAATAGAAACATTAT TGTTAAAGGACAGCATTAGTTCACAGTCAAACAAGCAAGATTGAGAATTAACCTTGGTTTTGAAC TTGAACACTTAGGGGATTGAAGATTCAACAACCCTAAAGCTTGGGGTAAAACATTGGAAATAGTT AAAAGACAAATTGCTCGGGTTTACCTGAGAGCCTACAACATGGATAAACGGGTGAGAGGTTCATT GGCGCCGAGTCTCACTGAATCTGACATGGATTACCACAAGATCTTGACAGCAGGTCTGTCCGTTC AACAGGGGATTGTTCGGCAAAGAGTCATCCCAGTGTATCAAGTAAACAATCTTGAAGAAATTTGC CAACTTATCATACAGGCCTTTGAAGCAGGTGTTGATTTTCAAGAGAGTGCGGACAGTTTCCTTCT CATGCTTTGTCTTCATCATGCGTACCAGGGAGATTACAAACTTTTCTTGGAAAGTGGCGCAGTCA AGTATTTGGAAGGGCACGGGTTCCGTTTTGAAGTCAAGAAGCGTGATGGAGTGAAGCGCCTTGAG GAATTGCTGCCAGCAGTATCTAGTGGAAAAAACATTAAGAGAACACTTGCTGCCATGCCGGAAGA GGAGACAACTGAAGCTAATGCCGGTCAGTTTCTCTCCTTTGCAAGTCTATTTCTACCCAAACTTG TCGTTGGAGAAAAGGCTTGCCTTGAGAAGGTTCAAAGGCAAATTCAAGTACATGCAGAGCAAGGA CTGATACAATATCCAACAGCTTGGCAATCAGTAGGACACATGATGGTGATTTTCCGTTTGATGCG AACAAATTTTCTGATCAAATTTCTCCTAATACACCAAGGGATGCACATGGTTGCCGGGCATGATG CCAACGATGCTGTGATTTCAAATTCAGTGGCTCAAGCTCGTTTTTCAGGCTTATTGATTGTCAAA ACAGTACTTGATCATATCCTACAAAAGACAGAACGAGGAGTTCGTCTCCATCCTCTTGCAAGGAC CGCCAAGGTAAAAAATGAGGTGAACTCCTTTAAGGCTGCACTCAGCTCCCTGGCCAAGCATGGAG AGTATGCTCCTTTCGCCCGACTTTTGAACCTTTCTGGAGTAAATAATCTTGAGCATGGTCTTTTC CCTCAACTATCGGCAATTGCACTCGGAGTCGCCACAGCACACGGGAGTACCCTCGCAGGAGTAAA TGTTGGAGAACAGTATCAACAACTCAGAGAGGCTGCCACTGAGGCTGAGAAGCAACTCCAACAAT ACGCAGAGTCTCGCGAACTTGACCATCTTGGACTTGATGATCAGGAAAAGAAAATTCTTATGAAC TTCCATCAGAAAAAGAACGAAATCAGCTTCCAGCAAACAAACGCTATGGTAACTCTAAGAAAAGA GCGCCTGGCCAAGCTGACAGAAGCTATCACTGCTGCGTCACTGCCCAAAACAAGTGGACATTACG ATGATGATGACGACATTCCATTTCCCGGGCCGATCTATGATGACGACAATCCTGGCCATCAAGAT GATGATCCGACTGACTCACAGGATACGACCATTCCCGATGGTGTTGTTGACCCGTATGATGGAAG CTACGGCGAATATCCTGACTACGAGGATTCGGCTGAAGGTGCACCAGATGACTTGGTCCTATTCG ATCTAGACGAGGACGACGAGGACACTAAGCCAGTGCCTAATAGATCGACCAAGGGTGGACAACAG AAGAACAGTCAAAAGGGCCAGCATATAGAGGGCAGACAGATCCGACCTTGGACGGAGCGAAAAAG GTGCCGGAGTTGCAGAACAATCCACCACGCCAGTGCGCCACTCACGGACAATGACAGAAGAAATG AACCCTCCGGCTCAACCAGCCCTCGCATGCTGACACCAATTAACGAAGAGGCAGACCCACTGGAC GATGCCGACGACGAGAGTCTCACATCCCTGCCCTTGGAGTCAGATGATGAAGAGCAGGACAGGGA CGGAACTTCCAACCGCACACCCACTGTCGCCCCACCGGCTCCCGTATACAGAGATCACTCTGAAA AGAAAGAACTCCCGCAAGACGAGCAACAAGATCAGGACCACACTCAAGAGGCCAGGAACCAGGAC AGTGACAACACCCAGTCAGAACACTCTTTTGAGGAGATGTATCGCCACATTCTAAGATCACAGGG GCCATTTGATGCTGTTTTGTATTATCACCTAATGAGTGATGAGCCTGTAGTTTTCAGTACCAGTG ATGGCAAAGAGTACACGTATCCAGACTCCCTTGAAGAGGAATATCCACCATGGCTCACTGAAAAA GAGGCTATGAATGAAGAGAATAGATTTGTTACATTGGATGGTCAACAATTTTATTGGCCGGTGAT GAATCACAAGAATAAATTCATGGCAATCCTGCAACATCATCAGTGAATGAGCATGGAACAATGGG ATGATTCAACCGACAAATAGCTAACATTAAGTAGTCAAGGAACGAAAACAGGAAGAATTTTTGAT GTCTAAGGTGTGAATTATTATCACAATAAAAGTGATTCTTATTTTTGAATTTAAAGCTAGCTTAT TATTACTAGCCGTTTTTCAAAGTTCAATTTGAGTCTTAATGCAAATAGGCGTTAAGCCACAGTTA TAGCCATAATTGTAACTCAATATTCTAACTAGCGATTTATCTAAATTAAATTACATTATGCTTTT ATAACTTACCTACTAGCCTGCCCAACATTTACACGATCGTTTTATAATTAAGAAAAAAGCGGCCG CAGAGCTC GP Chimeric sequence (SEQ ID NO: 1044): GGTACCCTCGAGGATGAAGATTAAGCCGACAGTGAGCGTAATCTTCATCTCTCTTAGATTATTTG TTTTCCAGAGTAGGGGTCGTCAGGTCCTTTTCAATCGTGTAACCAAAATAAACTCCACTAGAAGG ATATTGTGGGGCAACAACACAATGGGCGTTCTTAGCCTACTCCAATTGCCTCGTGATCGATTCAA GAGGACATCATTCTTTCTTTGGGTAATTATCCTTTTCCAAAGAACATTTTCCATCCCACTTGGAG TCATCCACAATAGCACATTACAGGTTAGTGAGATTGACCAGCTAGTCTGCAAGGATCATACTGAT ATGCCATCTGCAACTAAAAGATGGGGCTTCAGGTCCGGTGTCCCACCAAAGGTGGTCAATTATGA AGCTGGTGAATGGGCTGAAAACTGCTACAATCTTGAAATCAAAAAACCGGACGGGAGCGAATGCT TACCCGCAGCGCCAGACGGGATTCGGGGCTTCCCCCGGTGCCGGTATGTGCACAAAGTATCAGGA ACGGGACCGTGTGCCGGAGACTTTGCCTTCCATAAAGAGGGTGCTTTCTTCCTGTATGATCGACT TGCTTCCACAGTTATCTACCGAGGAACGACTTTCGCTGAAGGTGTCGTTGCATTTCTGATACTGC CCCAAGCTAAGAAGGACTTCTTCAGCTCACACCCCTTGAGAGAGCCGGTCAATGCAACGGAGGAC CCGTCTAGTGGCTACTATTCTACCACAATTAGATATCAGGCTACCGGTTTTGGAACCAATGAGAC AGAGTACTTGTTCGAGGTTGACAATTTGACCTACGTCCAACTTGAATCAAGATTCACACCACAGT TTCTGCTCCAGCTGAATGAGACAATATATACAAGTGGGAAAAGGAGCAATACCACGGGAAAACTA ATTTGGAAGGTCAACCCCGAAATTGATACAACAATCGGGGAGTGGGCCTTCTGGGAAACTAAAAA AACCTCACTAGAAAAATTCGCAGTGAAGAGTTGTCTTTCACAGTTTTATCGCTCAACGAGACAGA CATCAGTGGTCAGAGTCCGGCGCGAACTTCTTCCGGAAGAATCTCCGACCGGGCCACTGAAGACC ACAAAATCATGGCTTCAGAAAATTCCTCTGCAATGGTTCAAGTGCACAGTCAAGGAAGGGAAACA ACATTGCCGTCTCAGAATTCGACAGAAGGTCGAAGAGCGAGTCCCCAATCCCTCACAACCAAACC AGGTCCGGACAACAGCACCCATAATACACCCGTGTATAAACTTGACATCTCTGAGGCAACTCAAG TTGAACAACATCACCGCAGAACAGACAACGACAGCACAGCCTCCGACACTCCCTCTGCCACGACC GCAGCCGGACCCCCAAAAGCAGAGAACACCAACACGAGCAAGAGCACTGACTTCCTGGACCCCGC CACCACAACAAGTCCCCAAAACCACAGCGAGACCGCTGGCAACAACAACACTCATCACCAAGATA CCGGAGAAGAGAGTGCCAGCAGCGGGAAGCTAGGCTTAATTACCAATACTATTGCTGGAGTCGCA GGACTGATCACAGGCGGGAGAAGAACTCGAAGAGAAGCAATTGTCAATGCTCAACCCAAATGCAA CCCTAATTTACATTACTGGACTACTCAGGATGAAGGTGCTGCAATCGGACTGGCCTGGATACCAT ATTTCGGGCCAGCAGCCGAGGGAATTTACATAGAGGGGCTAATGCACAATCAAGATGGTTTAATC TGTGGGTTGAGACAGCTGGCCAACGAGACGACTCAAGCTCTTCAACTGTTCCTGAGAGCCACAAC GGAGCTGCGGACATATACCATACTCAACCGTAAGGCAATTGATTTCTTGCTGCAGCGATGGGGCG GCACATGCCACATTCTGGGACCGGACTGCTGTATCGAACCACATGATTGGACCAAGAACATAACA GACAAAATTGATCAGATTATTCATGATTTTGTTGATAAAACCCTTCCGGACCAGGGGGACAATGA CAATTGGTGGACAGGATGGAGACAATGGATACCGGCAGGTATTGGAGTTACAGGCGTTATAATTG CAGTTATCGCTTTATTCTGTATATGCAAATTTGTCTTTTAGTTTTTCTTCAGATTGCTTCATGGA AAAGCTCAGCCTCAAATCAATGAAACCAGGATTTAATTATATGGATTACTTGAATCTAAGATTAC TTGACAAATGATAATATAATACACTGGAGCTTTAAACATAGCCAATGTGATTCTAACTCCTTTAA ACTCACAGTTAATCATAAACAAGGTTTGACATCAATCTAGTTATCTCTTTGAGAATGATAAACTT GATGAAGATTAAGAAAAAGCGGCCGCAGAGCTC The L gene was generated as 2 fragments (L-ABC, SEQ ID NO: 1049; and L-DEFG, SEQ ID NO: 1050). L fragment 1: SEQ ID NO: 1049 (L-ABC): GGCGCGCCTCGAGGAGGAAGATTAAGAAAAACTGCTTATTGGGTCTTTCCGTGTTTTAGATGAAG CAGTTGAAATTCTTCCTCTTGATATTAAATGGCTACCCAACATACACAATACCCAGACGCTAGTT ATCATCACCAATTGTATTGGACCAATGTGACCTAGTCACTAGAGCTTGCGGGTTATATTCATCAT ACTCCCTTAATCCGCAACTACGCAACTGTAAACTCCCGAAACATATCTACCGTTTGAAATACGTG TAACTGTTACCAAGTTCTTGAGTGATGTACCAGTGGCGACATTGCCCATAGATTTCATAGTCCCA GTTCTTCTCAAGGCACTGTCAGGCAATGGATTCTGTCCTGTTGAGCCGCGGTGCCAACAGTTCTA GATGAAATCATTAAGTACACAATGCAAGATGCTCTCTTCTTGAAATATTATCTCAAAAATGTGGG TGCTCAAGAAGACTGTGTTGATGAACACTTTCAAGAGAAAATCTTATCTTCAATTCAGGGCAATG ATTTTTACATCAAATGTTTTTCTGGTATGATCTGGCTATTTTAACTCGAAGGGGTAGATTAAATC GAGGAAACTCTAGATCAACATGGTTTGTTCATGATGATTTAATAGACATCTTAGGCTATGGGGAC TTGTTTTTTGGAAGATCCCAATTTCAATGTTACCACTGAACACACAAGGAATCCCCCATGCTGCT ATGGACTGGTATCAGGCATCAGTATTCAAAGAAGCGGTTCAAGGGCATACACACATTGTTTCTGT TTTACTGCCGACGTCTTGATAATGTGCAAAGATTTAATTACATGTCGATTCAACACAACTCTAAT CTCAAAAATAGCAGAGATTGAGGATCCAGTTTGTTCTGATTATCCCAATTTTAAGATTGTGTCTA TGCTTACCAGAGCGGAGATTACTTACTCTCCATATTAGGGTCTGATGGGTATAAAATTATTAAGT TCCTCGAACCATTGTGCTTGGCCAAAATTCAATTATGCTCAAAGTACACTGAACGAAAAGGGCGG TTTTAACACAAATGCATTTAGCTGTAAATCACACCCTAGAAGAAATTACAGAAATGCGTGCACTA AAGCCTTCACAGGCTCAAAAGATCCGTGAATTCCATAGAACATTGATAAGGCTGGAGATGACGCC ACAACACTTTGTGAGCTATTTTCCATTCAAAAACACTGGGGGCATCCTGTGCTACATAGTGAAAC AGCAATCCAAAAAGTTAAAAAACATGCTACGGTGCTAAAAGCATTACGCCCTATAGTGATTTTCG AGACATCTGTGTTTTTAAATATAGTATTGCCAAACATTATTTTGATAGTCAAGGATCTTGGTACA GTGTTACTTCAGACCGATGTTTAACGCCGGGATTGAATTCTTATATCAAAAGAAATCAATTCCCT CCGTTGCAATGATTAAAGAACTACTATGGGAATTTTACCACCTTGACCACCCTCCACTTTTCTCA ACCAAAATTATTAGTGACTTAAGTATTTTTATAAAAGACAGAGCTACCGCAGTAGAAAGGACATG CTGGGATGAGTATTCGAGCCTAATGTTCTAGGATATAATCCACCTCACAAATTTAGTACTAAACG TGTACCGGAACAATTTTTAGAGCAAGAAAACTTTTCTATTGAGAATGTTCTTTCATACGCCCAAG AACTTAGGTTCTACTACCACAATATCGGAACTTTTCTTTCTCATTGAAAGAGAAAGAGTTGAATG TAGGTAGAACCTTCGGAAAATTGCCTTATCCGACTCGCAATGTTCAAACACTTTGTGAAGCTCTG TTAGCTGATGTCTTGCTAAAGCATTTCCTAGCAATATGATGGTAGTTACGGAACGTGAGCAAAAA GAAAGCTTATTGCATCAAGCATCATGGCACCACACAAGTGATGATTTTGGTGAACATGCCACAGT TAGAGGGAGTACTTTGTAACTGATTTAGAGAAATACAATCTTGCATTTAGATATGAGTTTACAGC ACCTTTTATAGAATATTGCAACCGTTGCTATGGTGTTAAGAATGTTTTTAATTGGATGCATTATA CAATCCCACAGTTTATATGCATGTCAGTGATTATTATAATCCACCACATAACCTCACACTGGAGA ATCGAGACAACCCCCCCGAAGGGCCTAGTTCATACAGGGGTCATATGGGAGGGATTGAAGGACTG CAACAAAAACTCTGACAAGTATTTCATGTGCTCAAATTTCTTTAGTTGAAATTAAGACTGGTTTT AAGTTACGCTCAGCTGTGATGGGTGACAATCAGTGCATTACTGTTTTATCAGTCTTCCCCTTAGA GACTGACGCAGACGGCAGGAACAGAGCGCCGAAGACAATGCAGCGAGGGTGGCCGCCAGCCTAGC AAAAGTTACAAGTGCCTGTGGAATCTTTTTAAAACCTGATGAGACTTTCGTACACTCAGGTTTTA TCTATTTTGGAAAAAACAATATTTGAATGGGGTCCAATTGCCTCAGTCCCTTAAAACGGCTACAA GAATGGCACCATTGTCTGATGCAATTTTTGATGATCTTCAAGGGACCCTGGCTAGTATAGGCACT GCTTTTGAGCGATCAACTCCGAAACTAGACATATCTTTCCTTGCAGGATAACCGCAGCTTTCCAT ACGTTTTTTTCGGTGAGAATCTTGCAATATCATCATCTCGGGTTCAATAAAGGTTTTGACCTTGG ACAGTTAACACTCGGCAACCTCTGGATTTCGGAACAATATCATTGGCACTAGCGGTACCGCAGGT GCTTGGAGGGTTATCCTTCTTGAATCCTGAGAAATGTTTCTACCGGAATCTAGGAGATCCAGTTA CCTCAGGCTTATTCCAGTAAAAACTTATCTCCGAATAGAGACCTATTGAGCTCCACCGCGGTGGC GGCCGCTCTAGCCCGGGCGGATCCCCCGGGCTGCAGGAATTCGATATCAAGCTTATCGATACCGT CGACCTCGAGGGGGGGCCCGTACCTTACATCGCGTTAATTAACTAGTGGATCGATCCCCAATTCG L fragment 2: SEQ ID NO: 1050 (L-DEFG): CGCGACGTAATACGACTCACTATAGGGCGAATTGGGCGCGCCCCGTCTCAGAATGATTGAGATGG ATGATTTATTCTTACCTTTAATTGCGAAGAACCCTGGGAATTGTAGCGCAATTGACTTTGTGTAA ATCCTAGCGGATTAAATGTCCCTGGGTCGCAAGACTTAACTTCATTTCTGCGCCAGATTGTACGC AGGACCATCACCCTAAGTGCGAAAAACAAACTTATTAATACCTTATTTCATGCGTCAGCTGACTC GAAGACGAAATGGTTTGTAAATGGCTATTATCATCAACTCCTGTTATGAGTCGTTTTGCGGCCGA TATCTTTTCACGCACGCCGAGCGGGAAGCGATTGCAAATTCTAGGATACCTGGAAGGAACACGCC ATTATTAGCCTCTAAGATCATCAACAATAATACAGAGACACCGGTTTTGGACAGACTGAGGAAAA TAACATTGCAAAGGTGGAGCCTATGGTTTAGTTATCTTGATCATTGTGATAATATCCTGGCGGAG CTTTAACCCAAATAACTTGCACAGTTGATTTAGCACAGATTCTGAGGGAATATTCATGGGCTCAT ATTTTAGAGGGAAGACCTCTTATTGGAGCCACACTCCCATGTATGATTGAGCAATTCAAAGTGTT TGGCTGAAACCCTACGAACAATGTCCGCAGTGTTCAAATGCAAAGCAACCAGGTGGGAAACCATT CGTGTCAGTGGCAGTCAAGAAACATATTGTTAGTGCATGGCCGAACGCATCCCGAATAAGCTGGA CTTCGGGGATGGAATCCCATACATTGGATCAAGGACAGAAGATAAGATAGGTCAGCCCGCTATTA AGCCGAGGTGTCCTTCCGCAGCCTTAAGAGAGGCCATTGAATTGGCGTCCCGTTTAACATGGGTA ACTAAGGCAGTTCGAACAGTGACTTGCTAATAAAACCATTTTTGGAAGCACGAGTAAATTTAAGT GTTCAAGAAATACTTCAAATGACCCCTTCACATTACTCAGGAAATATTGTGCATCGGTATAACGA TCAAACAGTCCTCATTCTTTCATGGCCAATCGTATGAGTAATTCAGCAACGCGCTTGATGGTATC TACAAACACTTTAGGTGAGTTTTCAGGAGGTGGCCAGTCTGCACGCGACAGCAATATTATTTTCC AGAATTTATAAATTATGCAGTTGCACTGTTCGATATTAAATTTAGAAACACTGAGGCTACAGATA TCCAATATAATCGTGCTCACCTTCATCTAACTAAGTGTTGCACCCGGGAAGTACCAGCTCAGTAT TTAACAACACAACCACGCTAAATCTAGATTTAACAAGATACCGAGAAAACGAATTGATTTATGAC AGTAATCCTCTAAAAGGAGGACTCAATTGCAACTTATCGATTGACAGTCCTTTTTTCCAAGGTAA ACGGCTGACATTATAGAAGATGATCTTATTCGACTGCCTCACTTATCTGGATGGGAGCTAGCCAA GACCATCATGCAATCAATTATTTCAGATAGCAACAATTCATCTACAGACCCAATTAGCAGTGGAG AAACAAGACATTCACTACCCATTTCTTAACTTATCCCAAGATAGGACTTCTGTACAGTTTTGGGG CCTTTGTAAGTTATTATCTTGGCAATACAATTCTTTGCACGAAAAAGATCGGACTTGACAATTTT TTATATTACTAACTACTCAAATTCATAATCTACCACATCGCTCATTGCGAATACTTAAGCCAACA TTCAAACATGCAAGCGTTATGTCACGGTTAATGAGTATTGATCCTCATTTTTCTATTTACATAGG CGGTGCTGCAGTGACAGAGGACTCTCAGATGCGGCCAGGTTATTTTTGAGAACGTCCATTTCATC TTTTCTTACATTTGTAAAAGAATGGATAATTAATCGCGGAACAATTGTCCCTTTATGGATAGTAT ATCCGCTAGAGGTCAAAACCCAACACCTGTGAATAATTTTCTCTATCAGATCGTAGAACTGCTGG TGCATGATTCATCAAGACAACAGGCTTTTAAAACTACCATAAGTGATCATGTACATCCTCACGAC AATCTTGTTTACCATGTAAGAGTACAGCCAGCAATTTCTTCCATGCATCATTGGCGTACTGGAGG AGCAGACACAGAAACAGCAACCGAAAATACTTGGCAAGAGACTCTTCAACTGGATCAAGCACAAA CAACAGTGATGGTATATTGAGAGAAGTCAAGAACAAACCACCAGAGATCCACATGATGGCACTGA ACGGAATCTAGTCCTACAAATGAGCCATGAAATAAAAAGAACGACAATTCCACAAGAAAACACGC ACCAGGGTCCGTCGTCCAGTCCTTTCTAAGTGACTCTGCTTGTGGTACAGCAAATCCAAAACTAA ATTTCGATCGATCGAGACACAATGTGAAATTTCAGGATCATAACTCGGCATCCAAGAGGGAAGGT CATCAAATAATCTCAACCGTCTAGTCCTACCTTTCTTTACATTATCTCAAGGGACACGCCAATTA ACGTCATCCAATGAGTCACAAACCCAAGACGAGATATCAAAGTACTTACGGCAATTGAGATCCGT CATTGATACTACCATAATTGTCGCTTCACCGGTATAGTCTCGTCCATGCATTACAAACTTGATGA GGTCCTTTGGGAAATAGAGAGTTTCAAGTCGGCTGTGACGCTAGCAGAGGGAGAAGGTGCTGGTG CCTTACTATTGATTCAAAATACGGCGTTAAGAAGTTATTTTTCAACACGCTAGCTACTGAGTCCA GTATAGAGTCAGAAATAGTATCAGGAATGACTACTCCTAGGATGCTTCTACCTGTTATGTCAAAA TTCCATAATGACCAAATTAGATTATTCTTAACAACTCAGCAAGCCAAATAACAGACATAACAAAT CCTACTTGGTTTAAAGACCAAAGAGCAAGGCTACCTAAGCAAGTCGAGGTTATAACCATGGATGC AGAGACAACAGAGAATATAACAGATCGAAATTGTACGAAGCTGTATATAAATTGATCTTACACCA TATTGATCCTAGCGTATTGAAAGCAGTGGTCCTTAAAGTCTTTCTAAGTGATACTGAGGGTATGT TATGGCTAAATGATAATTTACCCCGTTTTTTGCCACTGGTTATTTAATTAAGCCAATAACGTCAA GTGCTAGATCTAGTGAGTGGTATCTTTGTCTGACGAACTTCTTATCAACTACACGTAAGATGCCA CACCAAAACCATCTCAGTTGTAACAGGTAATACTTACGGCATTGCAACTGCAAATTCAACGAAGC CCATACTGGCTAAGTCATTTAACTCAGTATGCTGACTGTGAGTTACATTTAAGTTATATCCGCCT TGGTTTTCCATCATTAGAGAAATACTATACCACAGGTATAACCTCGTCGATTCAAAAAGAGGTCC ACTAGTCTCTATCACTCAGCACTTAGCACATCTTAGAGCAGAGATTCGAGAATTAACTAATGATT ATAATCAACAGCGACAAAGTCGACCCAGACTTATCATTTTATTCGTACTGCAAAAGGACGGATAA CTAAACTAGTCAATGATTATTTAAAATTCTTTCTTATTGTGCAAGCATTAAAACATAATGGGACA TGGCAAGCTGAGTTTAAGAAATTACAGAGTTGATTAGTGTGTGCAATAGGTTCTACCATATTAGA GATTGCAATTGTGAAGAACGTTTCTTAGTTCAAACCTTATATTTACATAGAATGCAGGATTCTGA AGTTAAGCTTATCGAAAGGCTGACAGGCTTCTGAGTTTATTTCCGGATGGTCTCTACAGGTTTGA TTGAATTACCGTGCATAGTATCCTGATACTTGCAAAGGTTGGTTATTAACATACAGATTATAAAA AAGCGGCCGCAGAGCTCCAGCGGTGGGGCCGCCGGCGTCTAGCCCGGGCGGATCCCTGCAGGAAT TCGATATCAAGCTTATCGATACCGTCGACCTCGAGGGCCCATGCAGGCCGGCCAGGTACCTTAGT TAATTAACAGCTTTTGTTCCCTTTAGTAGGGTTAATTGACGCGCTC VP24 (SEQ ID NO: 1045): GGCGCGCCTCGAGGATGAAGATTAATGCGGAGGTCTGATAAGAATAAACCTTATTATTCAGATTA GGCCCCAAGAGGCATTCTTCATCTCCTTTTAGCAAAGTACTATTTCAGGGTAGTCCAATTAGTGG CACGTCTTTTAGCTGTATATCAGTCGCCCCTAGGCTAGGGTTTATAGTTGTCTCTAAGCTAAATT GGTCTTGAACTAGTCTACTCGCAGAATCCTACCGGGAATAGACTAATTGAACTTAGCCGTTTAAA ATTTAGTGCATAAATCTGGGCTAACACCACCAGGTCAACTCCATTGGCTGAAAAGAAGCTTACCT ACAACGAACATCACTTTGAGCGCCCTCACAATTAAAAAATAGGAACGTCGTTCCAACAATCGAGC GCAAGGTTTCAATATTATACGGGTCCATTAATTTCAACAAAATATTGATACTCCAGACACCAAGC AAGACCTGAGAAAAAACCATGGCTAAAGCTACGGGACGATACAATCTAATATCGCCCAAAAAGGA CCTGGAGAAAGGGGTTGTCTTAAGCGACCTCTGTAACTTCTTAGTTAGCCAAACTATTCAGGGGT GGAAGGTTTATTGGGCTGGTATTGAGTTTGATGTGAACCAAAAGGGTATTACCCTATTGCATAGA CTGAAAACTAATGACTTTGCCCCTGCATGGTCAATGACAAGGAATCTCTTTCCTCATTTATTTCA AAATCCGAATTCCACAATTGAATCACCGCTGTGGGCATTGAGAGTCATCCTTGCAGCAGGGATAC AGGACCAGCTGATTGACCAGTCTTTGATTGAACCCTTAGCAGGAGCCCTTGGTCTGATCTCTGAT TGGCTGCTAACAACCAACACTAACCATTTCAACATGCGAACACAACGTGTCAAGGAACAATTGAG CCTAAAAATGCTGTCGTTGATTCGATCCAATATTCTCAAGTTTATTAACAAATTGGATGCTCTAC ATGTCGTGAACTACAACGGATTGTTGAGCAGTATTGAAATTGGAACTCAAAATCATACAATCATC ATAACTCGGACTAATATGGGTTATCTTGTCGAGCTCCAAGAACCCGACAAATCTGCGATGGATAT ACGACACCCTGGGCCGGCGAAATTTTCCTTACTACATGAATCGACACTTAAAGCATTTACACAAG GATCCTCGACACGAATGCAAAGTTTGATTCTTGAATTTAATAGCTCTCTTGCTATCTAACTAAGG TAGAAAAAATTGTACGATAGGGCTAACATTATGCTGACTCAATAGTTATCTTGACATCTCTGCTT TCATAATCAGATATATAAGCATAATAAATAAATACTCATATTTCTTGATAATTTGTTTAACCACA GATAAATCCTCACTGTAAGCCAGCTTCCAAGTTGACACCCTTACAAAAACCAGGACTCAGAATCC CTCAAACAAGAGATTCCAAGACAACATCATAGAATTGCTTTATTATATGAATAAGCATTTTATCA CCAGAAATCCTATATACTAAATGGTTAATTGTAACTGAACCCGCAGGTCACATGTGTTAGGTTTC ACAGATTCTATATATTACTAACTCTAGAGCCCAAATTAACACGGTATAAGTAGATTAAGAAAAAA GCCTGAGGAAGATTAAGAAAAAGCGGCCGCATTAATTAA VP30 (SEQ ID NO: 1046): GGCGCGCCTCGAGGATGAAGATTAAGAAAAAGGTAATCTTTCGATTATCTTTAATCTTCATCCTT GATTCTACAATCATGACAGTTGTCTTTAGTGACAAGGGAAAGAAGCCTTTTTATTAAGTTGTAAT AATCAGATCTGCGAACCGGTAGAGTTTAGTTGCAACCTAACACACATAAAGCATTGGTCAAAAAG TCAATAGAAATTTAAACAGTGAGTGGAGACAACTTTTAAATGGAAGCTTCGTGAGCGCGGGAGAT CAAGGAATTCACGTGCCGACCAGCAAGGGATGGACACGACCACCATGTTCGAGCACGATCATCAT CCAGAGAGAATTATCGAGGTGAGTACCGTCAATCAAGGAGCGCCTCACAAGTGCGCGTTCCTACT GTATTTCATAAGAAGAGAGTTGAACCATTAACAGTTCCTCCAGCACCTAAAGACATATGTCCGAC CTTGAAAAAAGGATTTTTGTGTGACAGTAGTTTTTGCAAAAAAGATCACCAGCTTGAAAGCCTAA CCGACCGGGAATTACTCCTACTAATCGCCCGTAAGACTTGTGGATCAGTTGATTCATCGCTTAAT ATAACTGCACCCAAGGACTCGCGCTTAGCAAATCCAACGGCTGATGATTTCCAGCAAGAGGAAGG TCCAAAAAATTACTAGTCGAGACTGCTCAAGACGGCAGAACACTGGGCGAGACAAGACATCAGAA CCATAGAGGATTCAAAATTAAGAGCATTGTTGACTCTATGTGCTGTGATGACGAGGAAATTCTCA AAATCCCAGCTGAGTCTTTTATGTGAGACACACCTAAGGCGCGAGGGGCTTGGGCAAGATCAGGC AGAACCCGTTCTCGAAGTATATCAACGATTACACAGTGATAAAGGAGGCAGTTTTGAAGCTGCAC TATGGCAACAATGGGACCGACAATCCCTAATTATGTTTATCACTGCATTCTTGAATATTGCTCTC CAGTTACCGTGTGAAAGTTCTGCTGTCGTTGTTTCAGGCCTACGCTTACTTGCCCCCCCAAGCGT TAATGAAGAAGCTTCAACCAACCCGGGGACATGCTCATGGTCTGATGAGGGTACCCCTTAATAAG GCTGACTAAAACACTATATAACCTTCTACTTGATCACAATACTCCGTATACCTATCATCATATAT TTAATCAAGACGATATCCTTTAAAACTTATTCAGTACTATAATCACTCTCGTTTCAAATTAATAA GATGTGCATGATTGCCCTAATATATGAAGAGGTATGATACAACCCTAACAGTGATCAAAGAAAAT CATAATCTCGTATCGCTCGTAATATAACCTGCCAAGCATACTCCCTAGAAGCGTTGAATCTTGTA CACAAATAATGTTTTACTCTACAGGAGGTAGCAACGATCCATCCCATCAAAAAATAAGTATTTCA TGACTTACTAATGATCTCTTAAAATATTAAGAAAAAGCGGCCGCATTAATTAA VP35 (SEQ ID NO: 1047): GGTACCGCGATCGCGATGAAGATTAAAACCTTCATCATCCTTACGTCAATTGAATTCTCTAGCAC TCGAAGCTTATTGTCTTCAATGTAAAAGAAAAGCTGGTCTAACAAGATGACAACTAGAACAAAGG GCAGGGGCCATACTGCGGCCACGACTCAAAACGACAGAATGCCAGGCCCTGAGCTTTCGGGCTGG ATCTCTGAGCAGCTAATGACCGGCAAAATACCGCTAACCGACATCTTCTGTGATATTGAGAACAA TCCAGGATTATGCTACGCATCCCAAATGCAACAAACGAAGCCAAACCCGAAGACGCGCAACAGTC AAACCCAAACGGACCCAATTTGCAATCATAGTTTTGAGGAGGTAGTACAAACATTGGCTTCATTG GCTACAGCTGTGCGTCGGCAAACCATCGCATCAGAATCATTAGAACAACGCATTACGAGTCTTGA GAATGGTCTAAAGCCAGTTTATGATATGGCAAAAACAATATCATCCCTGAATCGCAGCTGTGCTG AGATGGTTGCAAAATATGATCTTCTGGTGATGACAACCGGTCGGGCAACAGCAACCGCTGCGGCA ACTGAGGCTTATTGGGCCGAACATGGTCAACCACCACCAGGCCCATCATTGTACGAGGATGGTGC GATTCGGGGTAAATTGAAAGATCCGAACGGGACCGTCCCTCAAAGTGTTAGGGAGGCATTCAACA ATCTAAACAGTACCACTTCACTAACTGAGGAAAATTTCGGGCGACCTTACATTTCGGCAAAGGAT TTGAGAAACATTATGTATGATCACTTGCCTGGTTTTGGAACTGCTTTCCACCAATTAGTACAAGT GATTTGTAAATTGGGAAAAGATAGCAACTCATTGGACATCATTCATGCTGAGTTCCAGGCCAGCC TGGCTGAAGGAGACTCTCCTCAATGTGCCCTAATTCAAATTACAAAAAGAGTTCCAATCTTCCAA GATGCTGCTCCACCTGTCATCCACATCCGCTCTCGAGGTGACATTCCCCGAGCTTGCCAGAAAAG CTTGCGTCCAGTCCCACCATCGCCCAAGATTGATCGAGGTTGGGTATGTGTTTTTCAGCTTCAAG ATGGTAAAACACTTGGACTCAAAATTTGAGCCAATGTAAGCTCATTTTGCGATGGGCGAATAATA GCAGAGGCTTCAACTGCTGAACTATAGGGTACGTTACATTAATGATACACTTGTGAGTATCAGCC CTGGATAATATAAGTCAATCCTAATCAATTGATAATATTGTTCATATCTCGCTAGCAGCTTAAAA TATAAATGTAATAGGAGCTATATCTCTGACAGTATTATAATCAATTGTTATTAAGTAACCCAAAC CAAAAGTGATGAAGATTAAGAAAAAGCGGCCGCAGAGCTC VP40 (SEQ ID NO: 1048): GGTACCTCGAGGATGAAGATTAAGAAAAACCTACCTCGGCTGAGAGAGTGTTTTTTCATTAACCT TCATCTTGTAAACGTTGAGCAAAATTGTTAAAAATATGAGGCGGGTTATATTGCCTACTGCTCCT CCTGAATATATGGAGGCCATATACCCTGTCAGGTCAAATTCAACAATTGCTAGAGGTGGCAACAG CAATACAGGCTTCCTGACACCGGAGTCAGTCAATGGGGACACTCCATCGAATCCACTCAGGCCAA TTGCCGATGACACCATCGACCATGCCAGCCACACACCAGGCAGTGTGTCATCAGCATTCATCCTT GAAGCTATGGTGAATGTCATATCGGGCCCCAAAGTGCTAATGAAGCAAATCCCTATTTGGTTGCC TCTAGGTGTCGCTGATCAAAAGACCTACAGCTTTGACTCAACTACGGCCGCAATTATGCTCGCAT CTTATACGATCACCCATTTCGGCAAGGCAACCAACCCCCTCGTTAGAGTGAATCGACTGGGTCCT GGAATCCCGGATCATCCCCTCAGGCTCCTGCGAATTGGAAACCAGGCTTTCCTCCAGGAGTTCGT TCTTCCGCCAGTCCAACTACCCCAGTATTTCACCTTTGATTTGACAGCACTCAAACTGATCACCC AACCACTGCCTGCTGCAACATGGACCGATGACACTCCAACAGGATCAAATGGAGCGTTGCGTCCA GGAATTTCATTTCATCCAAAACTTCGCCCCATTCTTTTACCCAACAAAAGTGGGAAGAAGGGGAA CAGTGCCGATCTAACATCTCCGGAGAAAATCCAAGCAATAATGACTTCACTCCAGGACTTTAAGA TCGTGCCAATTGATCCAGCCAAGAGTATCATTGGGATCGAGGTGCCAGAAACTCTGGTCCACAAG CTGACCGGTAAGAAGGTGACTTCTAAAAATGGACAACCAATCATCCCTGTTCTTTTGCCAAAGTA CATTGGGTTGGACCCGGTGGCTCCAGGAGACCTCACCATGGTAATCACACAGGATTGTGACACGT GTCATTCTCCTGCAAGTCTTCCAGCTGTGATTGAGAAGTAATTGCAATAATTGACTCAGATCCAG TTTTATAGAATCTTCTCAGGGATAGCAACTCAATCGACTTTTAGGACCGTCCATTAGAGGAGACA CTTTTAATTGAAAAATGTACTAATCGGGTCAAGGACCATTGTCTTTTTTCTCTCCTAAATGTAGA ACTTAACAAAAGACTCATAATATACTTGTTTTTAAAGGATTGATTGATGAAAGAACATGCATAAG CGATCCATACTTCGCCCTACTATAATCAATACGGTGATTCAAATGTTAATCTTTCTCATTGCACA TACTTTTTGCCCTTATCCTCAAATTGCCTGCATGCTTACATCTGAGGATAGCCAGTGTGACTTGG ATTGGAAATGTGGAGAAAAAATCGGGACCCATTTCTAGGTTGTTCACAATCCAAGTACAGACATT GCCCTTCTAATTAAGAAAAAAGCGGCCGCAGAGCTC

Other embodiments are in the claims. 

1. A pharmaceutical composition for inhibiting the expression of a gene from an Ebola virus in an organism, comprising a double-stranded ribonucleic acid (dsRNA) and a lipid formulation comprising the cationic lipid of formula A:

where R₁ and R₂ are independently alkyl, alkenyl or alkynyl, and wherein each of R₁ and R₂ can be optionally substituted, and wherein R₃ and R₄ are independently lower alkyl or together form an optionally substituted heterocyclic ring; and wherein said dsRNA comprises at least two sequences that are complementary to each other and wherein a sense strand comprises a first sequence and an antisense strand comprises a second sequence comprising a region of complementarity which is substantially complementary to at least a part of a mRNA encoding Ebola, and wherein said region of complementarity is less than 30 nucleotides in length.
 2. The pharmaceutical composition of claim 1, wherein said first sequence of said dsRNA consists of the sequence of SEQ ID NO:1027, and said second sequence consists of the sequence of SEQ ID NO:1028.
 3. The pharmaceutical composition of claim 1, wherein said first sequence is selected from the group consisting of the sense sequences of Table 2 and said second sequence is selected from the group consisting of the antisense sequences of Table
 2. 4. The pharmaceutical composition of claim 1, wherein said dsRNA comprises at least one modified nucleotide.
 5. The pharmaceutical composition of claim 3, wherein said dsRNA comprises at least one modified nucleotide.
 6. The pharmaceutical composition of claim 4, wherein said modified nucleotide is chosen from the group of: a 2′-O-methyl modified nucleotide, a nucleotide comprising a 5′-phosphorothioate group, and a terminal nucleotide linked to a cholesteryl derivative or dodecanoic acid bisdecylamide group.
 7. The pharmaceutical composition of claim 4, wherein said modified nucleotide is chosen from the group of: a 2′-deoxy-2′-fluoro modified nucleotide, a 2′-deoxy-modified nucleotide, a locked nucleotide, an abasic nucleotide, 2′-amino-modified nucleotide, 2′-alkyl-modified nucleotide, morpholino nucleotide, a phosphoramidate, and a non-natural base comprising nucleotide. 8.-9. (canceled)
 10. A method for inhibiting the expression of a gene from an Ebola virus in a cell, the method comprising: (a) introducing into the cell the pharmaceutical composition of claim 1; and (b) maintaining the cell produced in step (a) for a time sufficient to obtain degradation of the mRNA transcript of a gene from the Ebola virus, thereby inhibiting expression of a gene from the Ebola virus in the cell.
 11. A method of treating, preventing or managing pathological processes mediated by Ebola expression comprising administering to a subject in need of such treatment, prevention or management a therapeutically or prophylactically effective amount of the pharmaceutical composition of claim
 1. 12. The pharmaceutical composition of claim 1, wherein the dsRNA targets the VP35 of Ebola.
 13. The pharmaceutical composition of claim 1, wherein said dsRNA, upon contact with a cell infected with Ebola virus, inhibits expression of a gene from the virus by at least 40% compared to a control.
 14. The pharmaceutical composition of claim 1, wherein said region of complementarity is 15-30 nucleotides in length.
 15. The pharmaceutical composition of claim 1, wherein said region of complementarity is 19-24 nucleotides in length.
 16. The pharmaceutical composition of claim 1, wherein R₁ and R₂ of formula A are independently selected from oleoyl, pamitoyl, steroyl, or linoleyl.
 17. The pharmaceutical composition of claim 1, wherein R₁ and R₂ of formula A are both linoleyl.
 18. The pharmaceutical composition of claim 1, wherein R₃ and R₄ of formula A are methyl.
 19. The pharmaceutical composition of claim 1, wherein the cationic lipid of formula A is 2,2-Dilinoleyl-4-dimethylaminoethyl-[1,3]-dioxolane.
 20. The pharmaceutical composition of claim 1, further comprising a neutral lipid, a sterol, a PEG, or a PEG-modified lipid.
 21. The pharmaceutical composition of claim 20, wherein said pharmaceutical composition comprises LNP09.
 22. The pharmaceutical composition of claim 20, wherein said pharmaceutical composition comprises Formulation M.
 23. A method of increasing life-span of, decreasing viral titre in, or sustaining platelet count in a subject infected with an Ebola virus, comprising administering to the subject the pharmaceutical composition of claim 1 in an amount sufficient to increase the life-span of, decreasing viral titre in, or sustaining platelet count in the subject. 24.-42. (canceled)
 43. A pharmaceutical composition for inhibiting the expression of a gene from an Ebola virus in an organism, comprising a double-stranded ribonucleic acid (dsRNA) and a lipid formulation comprising a compound of formula X, selected from the group consisting of:

; and wherein said dsRNA comprises at least two sequences that are complementary to each other and wherein a sense strand comprises a first sequence and an antisense strand comprises a second sequence comprising a region of complementarity which is substantially complementary to at least a part of a mRNA encoding Ebola virus, and wherein said region of complementarity is less than 30 nucleotides in length.
 44. The pharmaceutical composition of claim 43, wherein said first sequence of said dsRNA consists of the sequence of SEQ ID NO:1027, and said second sequence consists of the sequence of SEQ ID NO:1028. 45.-72. (canceled) 